Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA replication”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,189 records · Page 66Linked to original sources

Polyomavirus DNA replication in the pancreas and in a transformed pancreas cell line has distinct enhancer requirements.

The regulatory DNA (enhancer) of polyomavirus (Py) is a major determinant of tissue-specific DNA replication during acute infection of newborn mice. Previously, we reported that the combination of one of the two Py enhancers (A enhancer) and the repeated Moloney murine leukemia virus (Mo-MuLV) enhancer gave a chimeric Py genome (Py-MuLV) that replicates predominantly in the acinar cells of the pancreas, a tissue not permissive for wild-type PyA2 replication (R. Rochford, B. A. Campbell, and L. P. Villareal. Proc. Nat. Acad. Sci. USA 84:449-453,1987). In this report, we further examine the combined enhancer requirements for acinar cell-specific Py replication. We also compare enhancer requirements for Py replication in the acinar cells of the pancreas with those of a transformed acinar cell line (266-6 cells). The deletion of sequences within the A enhancer of Py-MuLV (nucleotides 5098 to 5132) results in a virus with 10-fold-reduced levels of pancreas-specific replication. The deletion, however, of one of the 72-bp repeated Mo-MuLV enhancer sequences from Py-MuLV results in a complete loss of pancreas-specific DNA replication. Thus, the Py A enhancer is required for efficient replication of Py in the pancreas without otherwise altering organ specificity, but both of the repeated copies of the Mo-MuLV enhancer are essential for pancreas-specific Py replication. In contrast to the enhancer requirements for in vivo pancreas replication, in transformed acinar cells (266-6), PyA2 wild-type replicated efficiently and the Py-MuLV recombinant replicated inefficiently. These data suggest that the cell-specific control of DNA replication is different between normal pancreas cells and their transformed cell line counterparts and that this difference is apparent in the enhancer requirement of cell-specific Py DNA replication.

Animals↗

Characterization of DNA synthesis at a restrictive temperature in the temperature-sensitive mutants, tsFT5 cells, that belong to the complementation group of ts85 cells containing a thermolabile ubiquitin-activating enzyme E1. Involvement of the ubiquitin-conjugating system in DNA replication.

A temperature-sensitive mutant defective in DNA replication, tsFT5, has been isolated from the mouse mammary carcinoma cell line FM3A. DNA synthesis in tsFT5 cells at a restrictive temperature (39 degrees C) has been characterized in detail. Incorporation of [3H]thymidine decreased rapidly after an increase in temperature to 39 degrees C and the incorporation was less than 20% and 10% of the initial level after 4 and 8 h, respectively. Analysis by DNA fiber autoradiography revealed that the initiation of DNA replication at the origin of the replicons was impaired in tsFT5 cells but that the DNA chain elongation rate of the mutant cells did not decrease at the nonpermissive temperature. tsFT5 cells were confirmed to belong to the complementation group which includes ts85 cells arrested mainly in the G2 phase at the nonpermissive temperature. It has been observed that the amount of ubiquintin-conjugated histone H2A (uH2A) in ts85 cells decreases at the nonpermissive temperature (Marunouchi, T., Yasuda, H., Matsumoto, Y., and Yamada, M. (1980) Biochem. Biophys. Res. Commun. 95, 126-131). The amount of uH2A in tsFT5 cells also decreased rapidly at 39 degrees C. This decrease occurred at the same time as or slightly preceding to reduction in DNA synthesis, and the reappearance of uH2A was followed by the restoration of DNA synthesis after the temperature was reduced. A similar temporal relationship between decrease in the amount of uH2A and reduction in DNA synthesis was observed in ts85 cells cultured at 39 degrees C. However, the rates of the decrease of uH2A and of the reduction in DNA synthesis in ts85 cells were slower than those observed in tsFT5 cells. A comparison of the thermolability of purified ubiquitin-activating enzyme E1s revealed that the E1 from ts85 cells had a thermolability intermediate between those of the E1 from tsFT5 cells and of the wild-type cells. A reduction in the phosphorylation of histone H1 was observed in tsFT5 cells cultured at 39 degrees C, but the reduction occurred several hours after the decrease in uH2A and the reduction in DNA synthesis.

Animals↗

The double-stranded DNA replication intermediates formed in Chironomus polytene chromosomes consist of two populations.

DNA replication in Chironomus larvae that 7 days earlier passed the red-head stage is investigated. When pulse-labelled polytene chromosomes are lysed at 25 degrees C there is an enzymatic release of double-stranded DNA replication intermediates from the chromosomes. The released DNA molecules can be divided into two populations by gel electrophoresis in 1.5% agarose gels, one population is centered around slice 18 and the other population os centered around slice 27. Moreover, it is possible to chase with cold thymidine the population of labelled DNA molecules centered around slice 27 into the population centered around slice 18. The intermediates are after a time-lag joined together to produce a high molecular weight DNA which is not released from the chromosomes during cell lysis. Furthermore, in animals treated with 5-fluorodeoxyuridine the intermediates are joined together to produce a double-stranded DNA with the size expected to replicons. In contrast it is known that in late fourth instar larvae there is no subfractionation in 1.5% agarose of the DNA replication intermediates. This indicates that there is a difference in the formation of intermediates in the same tissue at two developmental stages.

Animals↗

Complete in vitro DNA replication of SV40 chromatin in digitonin-treated permeable cells.

A permeable cell system has been developed by treatment with digitonin for studying in vitro DNA replication of chromatin. DNA replication of simian virus 40 nucleoprotein complexes (SV40 chromatin) in digitonin-treated permeable cells was analyzed by electrophoresis in agarose-gel. Autoradiography of the agarose-gel revealed that [32P]dCTP was incorporated in SV40 DNA I, II and replicating intermediates. The time course of the incorporation indicated the complete replication of SV40 DNA and chromatin with a full number of nucleosomes. The digitonin-treated permeable cell system will serve as a useful system for studying in vitro DNA replication of chromatin.

Animals↗

Peptide binding to Geminin and inhibitory for DNA replication.

Geminin binds to Cdt1 to ensure that DNA replication occurs only once during the cell cycle. To identify the peptide that binds to Geminin and thereby modifies the latter's ability to alter the DNA replication activity in human cancer cells, we screened a phage display library of random peptides in successive cycles of phage library panning and found one peptide sequence that bound to the 31-111 amino acid residues of Geminin. Delivery of this peptide sequence into the nucleus of HCT116 human colon cancer cells resulted in the suppression of BrdU incorporation. These results provide new insights into the function of Geminin and further validate Geminin as a potential therapeutic target in tumors.

Amino Acid Sequence↗

ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genome.

The origin recognition complex (ORC) binds replicators in the yeast S. cerevisiae in a manner consistent with it being an initiator protein for DNA replication. Two-dimensional (2D) gel techniques were used to examine directly initiation of chromosomal DNA replication in temperature-sensitive orc mutants. Unlike in wild-type cells, in orc2-1 and orc5-1 mutant cells, only a subset of replicators formed active origins of DNA replication at the permissive temperature. At the restrictive temperature, the number of active replicators was diminished further. Using a genetic screen, CDC6 was identified as a multicopy suppressor of orc5-1. 2D gel and biochemical analyses demonstrated that Cdc6p interacted functionally and physically with ORC. We suggest that ORC and Cdc6p form a prereplication complex at individual replicators and therefore cooperate to determine the frequency of initiation of DNA replication in the genome.

Cell Cycle Proteins↗

Formation of a complex between nucleolin and replication protein A after cell stress prevents initiation of DNA replication.

We used a biochemical screen to identify nucleolin, a key factor in ribosome biogenesis, as a high-affinity binding partner for the heterotrimeric human replication protein A (hRPA). Binding studies in vitro demonstrated that the two proteins physically interact, with nucleolin using an unusual contact with the small hRPA subunit. Nucleolin significantly inhibited both simian virus 40 (SV-40) origin unwinding and SV-40 DNA replication in vitro, likely by nucleolin preventing hRPA from productive interaction with the SV-40 initiation complex. In vivo, use of epifluorescence and confocal microscopy showed that heat shock caused a dramatic redistribution of nucleolin from the nucleolus to the nucleoplasm. Nucleolin relocalization was concomitant with a tenfold increase in nucleolin-hRPA complex formation. The relocalized nucleolin significantly overlapped with the position of hRPA, but only poorly with sites of ongoing DNA synthesis. We suggest that the induced nucleolin-hRPA interaction signifies a novel mechanism that represses chromosomal replication after cell stress.

Cell Compartmentation↗

Cell cycle, DNA replication, repair, and recombination in the dimorphic human pathogenic fungus Paracoccidioides brasiliensis.

DNA replication, together with repair mechanisms and cell cycle control, are the most important cellular processes necessary to maintain correct transfer of genetic information to the progeny. These processes are well conserved throughout the Eukarya, and the genes that are involved provide essential information for understanding the life cycle of an organism. We used computational tools for data mining of genes involved in these processes in the pathogenic fungus Paracoccidiodes brasiliensis. Data derived from transcriptome analysis revealed that the cell cycle of this fungus, as well as DNA replication and repair, and the recombination machineries, are highly similar to those of the yeast Saccharomyces cerevisiae. Among orthologs detected in both species, there are genes related to cytoskeleton structure and assembly, chromosome segregation, and cell cycle control genes. We identified at least one representative gene from each step of the initiation of DNA replication. Major players in the process of DNA damage and repair were also identified.

Cell Cycle↗

[Detailed model of semi-conservative DNA replication. Possible role of DNA-polymerase errors in fragmented copying of both matrix strands].

A model of semiconservative DNA synthesis is considered. The model is based on a suggestion that the synthesis proceeds in the course of one-directional stretching of both matrix strands through the replicase complex (replisome), or of one-directional movement of the replisome along the chromosome. Each nucleotide link of the matrix strand find itself successively in the section of RNA primer synthesis, in the section of DNA polymerase and in the control section of a proofreading 3' leads to 5' exonuclease. Deoxynucleoside incorrectly joined by DNA polymerase of the replisome to the 3'-OH end of growing chain are, as a rule, removed when transferred in the control section. Since the reverse movement is prohibited, the DNA polymerase loses the 3'-OH end of new DNA chain and proves to be incapable to continue the synthesis. It can be renewed only after a new RNA primer formation. For continuation of the DNA synthesis after an incorrect deoxynucleotide addition, replicase must take two more mistakes in succession: to retain the incorrect nucleotide and to join the next one to this unproperly arranged primer. Only in that case the non-complementary nucleotide in a new DNA chain can escape the action of proofreading exonucleases. Hence, according to the model under discussion, the frequency of mutations should be many times lower than that of incorrect nucleotide joinings. The latter results, as a rule, in DNA chain synthesis cessation and in fragments formation. Taking into consideration the frequency of spontaneous mutations in bacteria (about 10(-9) per base-pair), the frequency of non-complementary joinings during semiconservative synthesis can be suggested of the order 10(-3) in accordance with the average Okazaki fragments size of 1000 nucleotides. Another possible reason for periodical interruptions of semiconservative DNA synthesis and for fragments formation is a distortion of replisome structure, accompanying the release of the matrix strand being copied in the direction of already replicated chromosome region. Both mechanisms can participate concurrently in DNA fragments formation. If replisomes are attached to a cell membrane, the sites of chromosome that are also fastened in the membrane, in particular, the site of "origin", are to be replicated using some mobile replicase complex.

DNA Replication↗

The capacity of polyomavirus enhancer binding protein 2alphaB (AML1/Cbfa2) to stimulate polyomavirus DNA replication is related to its affinity for the nuclear matrix.

The nuclear matrix is thought to play an important role in the DNA replication of eukaryotic cells, although direct evidence for such a role is still lacking. A nuclear matrix-associated transcription factor, polyomavirus (Py) enhancer binding protein 2alphaB1 (PEBP2alphaB1) (AML1/Cbfa2), was found to stimulate Py replication through its cognate binding site. The minimal replication activation domain (RAD) was identified between amino acid (aa) 302 and aa 371 by using a fusion protein containing the GAL4 DNA binding domain (GAL4-RAD). In addition, the region showed affinity for the nuclear matrix and, on the basis of competition studies, binding activity for one or more proteins involved in the initiation of Py DNA replication. A leukemogenic chimeric protein, AML1/ETO(MTG8), which does not contain this region of PEBP2alphaB1/AML1, was also localized in the nuclear matrix fraction and competed for nuclear matrix association with PEBP2alphaB1 and GAL4-RAD. Moreover, AML1/ETO inhibited Py DNA replication stimulated by PEBP2alphaB1 and GAL4-RAD. The inhibition was specific for replication mediated by PEBP2alphaB1 and GAL4-RAD, and proportional to the degree of loss of these activators from the nuclear matrix, suggesting a requirement for nuclear matrix targeting in the stimulation of Py DNA replication by RAD. These results are the first to suggest a molecular link between the initiation of DNA replication and the nuclear matrix compartment.

Animals↗

A model for the spatio-temporal organization of DNA replication in mammalian cells.

The spatio-temporal organization of chromosomal DNA replication was analyzed using a model based on a "DNA unit" (or decondensation unit) hypothesis. The model is an extension of the fork movement theory of Huberman & Riggs (1968) and can account for a partially deterministic and partially stochastic order of DNA replication in chromosomes. It presumes that each chromosome is composed of DNA units that are arranged in sequence and that are replicated in parallel. A deterministic wave of chromatin decondensation propagates along the DNA unit continuously and progressively providing a field for the random activation of replication origin. Assignment of replication times to DNA compartments by a Monte Carlo method was programmed based on the model and the program was used to stimulate DNA synthesis rate curves that can be measured by the method of Dolbeare et al. (1983, 1985). The shape of the curve is shown to constrain possible parameter values of the model, which include the rate of fork movement, the fraction of chromatin that is decondensed at the start of S-phase, the initial number of origins activated, the rate at which new origins are activated, etc. The chromosomal organization that controls the molecular level of DNA replication is briefly reviewed and its relevance to the model is also discussed.

Algorithms↗

Induction of polyomavirus DNA replication by cyclic AMP and a tumor promoter.

The effects of reagents that stimulate the intracellular level of cyclic AMP (cAMP), and of a tumor promoter, on polyomavirus (Py) DNA replication were examined in a Py-transformed rat cell line, designated the LPT line. cAMP-stimulating reagents (forskolin and 3-isobutyl-1-methyl xanthine) were found to induce replication of Py DNA in normally growing LPT cells and to enhance replication of the viral DNA in cells exposed to suboptimal doses of UV light and mitomycin C (which have been previously shown to induce Py DNA replication in LPT cells). The tumor promoter 12-O-tetradecanoyl phorbol-13-acetate did not cause a significant induction in Py DNA replication when it was applied to the cells alone, but enhanced replication of the viral DNA when it was applied together with the cAMP-stimulating reagents. Cycloheximide, an inhibitor of protein synthesis, was found to inhibit the induction of Py DNA replication by the cAMP-stimulating reagents. Based on these data, and on previous studies of the Py enhancer, it is proposed that cAMP may induce synthesis of an enhancer-binding protein that causes Py DNA replication in LPT cells by binding and activating an enhancer element which is a component of the Py origin.

1-Methyl-3-isobutylxanthine↗

A cdc2-like protein is involved in the initiation of DNA replication in Xenopus egg extracts.

Extracts of Xenopus eggs efficiently initiate and complete chromosomal DNA replication in vitro, under normal cell cycle controls. Such extracts can be depleted of Xenopus p34cdc2, either by affinity depletion using the protein p13suc1 or by specific immunodepletion. Depleted extracts are incapable of initiating DNA replication, although they efficiently elongate replication forks initiated in undepleted extracts. Depletion of p34cdc2 does not prevent nuclear assembly, which is required for the initiation of DNA replication in this system. Activity can be restored to depleted extracts by readdition of p13suc1 eluates enriched for p34cdc2. These results demonstrate that p34cdc2, or a very closely related protein, is involved in the initiation of chromosomal DNA replication in the cell cycle of higher eukaryotes.

Animals↗

Resistance of adenoviral DNA replication to aphidicolin is dependent on the 72-kilodalton DNA-binding protein.

Aphidicolin is a highly specific inhibitor of DNA polymerase alpha and has been most useful for assessing the role of this enzyme in various replication processes (J. A. Huberman, Cell 23:647-648, 1981). Both nuclear DNA replication and simian virus 40 DNA replication are highly sensitive to this drug (Krokan et al., Biochemistry 18:4431-4443, 1979), whereas mitochondrial DNA synthesis is completely insensitive (Zimmerman et al., J. Biol. Chem. 255:11847-11852, 1980). Adenovirus DNA replication is sensitive to aphidicolin, but only at much higher concentrations. These patterns of sensitivity are seen both in vivo and in vitro (Krokan et al., Biochemistry 18:4431-4443, 1979). A temperature-sensitive mutant of adenovirus type 5 known as H5ts125 is able to complete but not initiate new rounds of replication at nonpermissive temperatures (P. C. van der Vliet and J. S. Sussenbach, Virology 67:415-426, 1975). When cells infected with H5ts125 were shifted from permissive (33 degrees C) to nonpermissive (41 degrees C) conditions, the residual DNA synthesis (elongation) showed a striking increase in sensitivity to aphidicolin. The temperature-sensitive mutation of H5ts125 is in the gene for the 72-kilodalton single-stranded DNA-binding protein. This demonstrated that the increased resistance to aphidicolin shown by adenovirus DNA replication was dependent on that protein. It also supports an elongation role for both DNA polymerase alpha and the 72-kilodalton single-stranded DNA-binding protein in adenovirus DNA replication. Further support for an elongation role of DNA polymerase alpha came from experiments with permissive temperature conditions and inhibiting levels of aphidicolin in which it was shown that newly initiated strands failed to elongate to completion.

Adenoviruses, Human↗

[DNA replication: mechanism and significance for general practice].

The maintenance of genetic information in a cell is ensured by essential macromolecular events called DNA replication and DNA repair. The cell possesses many control mechanisms that allow the optimal strategy under extreme physiological conditions. A cell that is in the process of replicating its DNA and faces a genotoxic stress such as UV-damage, X-ray damage and influences of mutagens will turn off DNA replication and instead turn on DNA repair mechanisms. We have learned in the last three years that in all these processes identical DNA synthetic enzymes are involved. They are, however, coordinated to the actually required metabolic events through a ring-shaped protein called proliferating cell nuclear antigen (PCNA). Exact knowledge of these protein-protein interactions will eventually open up novel therapeutic strategies against cancer.

Cell Transformation, Neoplastic↗

Nucleoskeleton and initiation of DNA replication in metazoan cells.

To determine whether or not initiation sites for DNA replication in mammalian cells are defined by association with nuclear structure, attachments between the nucleoskeleton and the hamster DHFR gene initiation zone were examined. Nucleoskeletons were prepared by encapsulating cells in agarose and then extracting them with a nonionic detergent in a physiological buffer. The fraction of DNA that remained following endonuclease digestion was resistant to salt, sensitive to Sarkosyl, and essentially unchanged by glutaraldehyde crosslinking. Although newly replicated DNA was preferentially attached to the nucleoskeleton, no specific sequence was preferentially attached within a 65 kb locus containing the DHFR gene, two origins of bi-directional replication and at least one nuclear matrix attachment region. Instead, the entire region went from preferentially unattached to preferentially attached as cells progressed from G1 to late S-phase. Thus, initiation sites in mammalian chromosomes are not defined by attachments to the nucleoskeleton. To further assess the relationship between the nucleoskeleton and DNA replication, plasmid DNA containing the DHFR initiation region was replicated in a Xenopus egg extract. All of the DNA associated with the nucleoskeleton prior to S-phase without preference for a particular sequence and was released upon mitosis. However, about half of this DNA was trapped rather than bound to the nucleoskeleton. Thus, attachments to the nucleoskeleton can form in the absence of either DNA replication or transcription, but if they are required for replication, they are not maintained once replication is completed.

Animals↗

Immortalization of xeroderma pigmentosum cells by simian virus 40 DNA having a defective origin of DNA replication.

A simian virus 40 (SV40) DNA fragment, encompassing the whole early region and having a defective origin of DNA replication, has been used to transform human fibroblast cells derived from two xeroderma pigmentosum (XP) patients. Two of the SV40-transformed XP cell lines, belonging to complementation group C, had acquired the characteristic of indefinite life-span in culture. These XP cell lines synthesize T antigen as shown by immunofluorescence and retain the high sensitivity to UV irradiation. Detailed karyotype analysis shows very few chromosomal changes, while the transfecting SV40 DNA is integrated into cellular DNA sequences. These are the first immortalized XP cell lines derived from complementation group C. In view of the extreme difficulty in obtaining immortalized human fibroblasts, we suggest a possible advantage of replication defective SV40 DNA molecules for immortalizing human fibroblast cells of any source.

Cell Line↗

Recent excitement in the DNA replication problem.

It is now possible to reproduce most of the reactions involved in DNA replication using prokaryotic enzymes in vitro. Such systems have revealed that DNA replication is a complex process depending on a relatively large number of proteins, and that nucleoside triphosphate hydrolysis energy is used at several discrete steps. Much of the complexity of DNA replication may arise from the need for extreme copying fidelity.

Adenosine Triphosphate↗