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Novel expression of mouse adenovirus type 1 early region 3 gp11K at late times after infection.

Mutations were introduced into mouse adenovirus type 1 (MAV-1) early region 3 (E3) initiator codons by homologous recombination between viral DNA and a plasmid containing a mutagenized E3 region. The resulting mutant virus, pmE312, contained ATG --> TTA mutations at codon positions 1 and 4 and was expected to be null for the expression of the E3 proteins. However, gp11K, an MAV-1 E3 glycoprotein of 14K molecular weight, was detected in mutant-infected cell lysates at levels about 10-12% of that of wild-type (wt) virus at late times in infection. The gp11K polypeptide produced by pmE312 at late times was immunoprecipitated with two E3-specific antisera prepared against different regions of the protein. Like gp11K produced by wt virus infections, it was sensitive to endoglycosidase H (endo H) and thus resident in the endoplasmic reticulum (ER). In pmE312-infected cells treated with cytosine arabinoside (araC), an inhibitor of DNA replication, the gp11K protein was not detected by immunoprecipitation. This indicates that gp11K expression in pmE312-infected cells at late times was dependent on DNA replication and that it was thus translated from a late transcript. In vitro translation of poly(A)+ RNA from mock-, wild-type-, and pmE312-infected cells showed that gp11K was translated from late mRNA as an approximately 28K fusion between a late protein and gp11K. Our data are consistent with a model in which gp11K is expressed at late times as a late protein-gp11K chimera in both wt- and mutant-infected cells. This chimera is then processed: removal of a large N-terminal sequence results in the observed 14K ER-localized gp11K.

Adenoviridae↗

Large domains of apparent delayed replication timing associated with triplet repeat expansion at FRAXA and FRAXE.

Trinucleotide repeat expansions have been implicated in the causation of a number of neurodegenerative disorders. In the case of fragile X syndrome, full expansion of the FMR1 repeat element (CGG)n has also been correlated with replication timing delay of the locus and proximal flanking sequences in male lymphoblasts. To define more extensively this altered region of DNA replication, as well as to extend these studies to female cells containing premutant and mutant alleles, study of the replication timing properties of a >2-Mb zone in the FRAXA region (Xq27.3-q28) was undertaken by using a FISH technique. In this assay, relative times of replication of specific loci are inferred from the ratios of singlet and doublet hybridization signals in interphase nuclei. In all individuals with a full expansion of the trinucleotide repeat, a large (1-1.2-Mb) region of delayed timing was observed; the apparent timing of the earlier-replicating allele in female cells in this region was intermediate between normal and affected alleles in males, which is in accordance with expectations of a mixed population of cells resulting from random X inactivation. In addition, expansion of the nearby FRAXE locus also was found to correlate with replication timing delay, although the extent of the altered region was somewhat less. Trinucleotide repeat expansion thus may be acting in the Xq27.3-q28 region to alter long-range chromatin structure that could influence transcription of gene sequences within the affected domain.

Cells, Cultured↗

Late DNA replication in male mouse meiotic chromosomes.

Parts of the male mouse meiotic complement comprising the Y chromosome, the whole X chromosome, and near-centromeric parts of autosomal bivalents are synthesized late, as judged by tritiated thymidine autoradiography. This confirms the occurrence of end-to-end association between X and Y chromosomes and suggests that paired heterochromatic segments in autosomes must synthesize DNA at the same time.

Animals↗

Cutting, splicing, reordering, and elimination of DNA sequences in hypotrichous ciliates.

Hypotrichous ciliates extensively process genomic DNA during their life cycle. Processing occurs after cell mating, beginning with multiple rounds of DNA replication to form polytene chromosomes. Thousands of transposonlike elements are then excised from the chromosomes and destroyed, and thousands of short, internal eliminated sequences (IESs) are excised from coding and noncoding parts of genes and destroyed. IES removal from a gene is accompanied by splicing of the remaining chromosomal DNA segments to form a transcriptionally competent gene. For some genes these DNA segments are in a scrambled order and are ligated into a genetically correct order at the time of IES removal. Next the polytene chromosomes are cut up band-by-band and all genes are excised from the chromosomes as short, linear molecules averaging 2.2 kbp (in Oxytricha nova). Gene excision is accompanied by destruction of all nongenic DNA, which, together with the transposonlike elements and IESs, accounts for approximately 95% of the total sequence complexity of the genome in O. nova. Telomeric sequences are added to the excised gene-sized DNA molecules. Finally, the gene-sized molecules are replicated several times to form the macronucleus of the organism.

Actins↗

Replication timing properties of the human HPRT locus on active, inactive and reactivated X chromosomes.

X chromosome inactivation is associated with a highly asynchronous pattern of DNA replication at most X-linked loci in females. We studied the human HPRT locus, which is subject to X inactivation and expressed from only the active homolog, with the goal of comparing replication properties between the active and inactive homologs in this region using a fluorescence in situ hybridization approach. We found that in normal female lymphoblasts this locus is replicated in a highly asynchronous manner across a broad, discrete 500-600 kb zone with earliest replication appearing at the gene coding sequence. This general timing profile is maintained in normal male lymphoblasts, as well as in hamster x human hybrid cells containing the active human X chromosome. However, the inactive human X chromosome in the hamster cell background does not appear to function in a fully equivalent manner to the normal inactive X chromosome in female cells. Furthermore, reactivation of the inactive human X chromosome in a hamster x human hybrid system by 5-azacytidine treatment and HAT selection restores early replication at the HPRT gene itself, but does not change the overall domain behavior.

Animals↗

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription.

We describe an integrative data-driven mathematical framework that formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the "basis" set. By using pseudoinverse projection, the molecular biological profiles of the data samples are least-squares-approximated as superpositions of the basis profiles. Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. We illustrate this framework with an integration of yeast genome-scale proteins' DNA-binding data with cell cycle mRNA expression time course data. Novel correlation between DNA replication initiation and RNA transcription during the yeast cell cycle, which might be due to a previously unknown mechanism of regulation, is predicted.

Cell Cycle↗

Origin and degradation of the RNA primers at the 5' termini of nascent DNA chains in Bacillus subtilis.

We had earlier characterized the nascent DNA synthesized in permeable cells of Bacillus subtilis in the presence of 5-mercurideoxycytidine triphosphate and 2',3'-dideoxyATP as being substituted at its 5' end with a ribonucleotide moiety of the sequence pApG(pC)1-2 DNA. In this paper, we examine the origin and turnover of the DNA-linked ribonucleotide and its relationship to DNA replication. At least 50% of the RNA-linked nascent DNA chains served as guanylate acceptors when incubated with GTP and the eukaryotic capping enzyme, indicating the presence of 5'-terminal di- or triphosphate groups and suggesting that the RNA moiety is synthesized de novo and is not a degradation product. In nascent DNA produced without limitation of chain growth by dideoxyATP, the degree of terminal ribonucleotide substitution was reduced by 50%, consistent with a linkage between RNA primer removal and DNA chain growth. Such a relationship was demonstrated directly by examining the RNA primer content of nascent DNA synthesized in the absence of dideoxyATP as a function of DNA chain length. As the DNA size increased from 40 to 200 nucleotide residues, the extent of RNA substitution declined from 80% to nearly 0%. Endgroup analysis showed that the loss of RNA was accompanied by a gradual shift from predominantly adenylate residues to 5'-terminal guanylate, consistent with a stepwise removal of ribonucleotides from the 5' end. Evidence that the nascent mercurated DNA synthesized under our experimental conditions was indeed a replicative intermediate came from the study of the time course of DNA chain growth and pulse-chase experiments. In the presence of the DNA ligase inhibitor NMN, mercurated DNA accumulated in two size classes with average length of approximately 750 and 8000 nucleotide residues, presumably representing the mature size of intermediates in discontinuous DNA synthesis. Comparison with the DNA size range at which the loss of the 5'-terminal RNA moiety occurred (40 to 200 residues) indicated that the processing of RNA primers occurred at an early stage during DNA chain elongation, and that moderate size intermediates in discontinuous DNA replication (greater than 200 nucleotides) have already lost their RNA primers.

Bacillus subtilis↗

Replication of transfected plasmid DNA by cells infected with African swine fever virus.

Recombinant plasmids containing African swine fever virus (ASFV) DNA fragments covering all the virus genome were transfected into infected cells in order to detect viral origins of DNA replication. Plasmid replication was monitored by sensitivity to MboI, which cleaves only replicated, unmethylated DNA, and resistance to DpnI, which cleaves only the same methylated sequence. All the recombinants replicated to a similar extent, indicating that ASFV does not use a preferred origin for DNA replication. Circular plasmids without viral inserts were also replicated, but linearized plasmids or lambda bacteriophage DNA were not replicated. Replicated plasmid DNA began to accumulate with a time course similar to viral DNA, starting between 6 and 12 hr p.i. and increasing steadily for about 18 hr. This apparent dependence on viral functions was confirmed by the sensitivity of plasmid replication to phosphonoacetic acid and resistance to aphidicolin and by the reduction of replication in cells infected with a mutant defective in DNA replication. Replicated plasmid DNA present as unit length circles and as large dimension forms, probably head-to-tail concatemers. The results of two-dimensional electrophoresis (neutral/alkaline) favor a rolling-circle mechanism for plasmid DNA replication.

African Swine Fever Virus↗

Initiation of deoxyribonucleic acid replication in Escherichia coli B: uncoupling from mass/deoxyribonucleic acid ratio.

In Escherichia coli growing at different rates, the ratio of cell mass to the number of chromosome origins tended to be constant at the time of the initiation of deoxyribonucleic acid (DNA) replication. This observation led to the assumption that the initiation event is controlled in some way by cell mass, e.g., by a growth-dependent synthesis of an initiator or dilution of a repressor. We have now found that the initiation of DNA synthesis can be uncoupled from cell mass. We used a synchronous culture of newly divided cells of E. coli B which was obtained by the membrane elution technique (C.E. Helmstetter, J. Mol. Biol. 24: 417-427, 1967) and was starved for an amino acid. Upon restoration of the amino acid, the cells not only divided at a size that was smaller than normal, but also initiated DNA replication long before they could increase their masses to reach the expected ratio of mass/DNA presumably required for initiation.

Acetates↗

[Inhibition of parvovirus H-1 on transplantable human hepatoma and its histological and histobiochemical studies].

A transplantable human hepatoma model, the QGY-9204, was used in this study. The growth kinetics of hepatoma in nude mice were compared after injection of parvovirus H-1 into the tumor growth. Significant difference in growth curves were seen between injected groups with H-1 dosages of 5 x 10(7) PFU and 5 x 10(8) PFU and that of control. It indicated that parvovirus H-1 was capable of suppressing the growth of human hepatoma. Previous studies showed H-1 is oncotropic, oncosuppressive and oncolytic. For histological, ultrastructural and histochemical examinations, transplantable hepatomas were taken at different time interval post H-1 (1 x 10(8) PFU per tumor growth) injection. For H-1 DNA amplification and H-1 nonstructural protein expression, PCR and ABC approach in hepatoma paraffin sections were used. The H-1 treated groups exhibited obvious signs of necrosis. It started on 3rd day post infection (3 d.p.i.) and the area of necrosis enlarged consecutively on 7 d.p.i., 10 d.p.i. and 14 d.p.i., but none was seen in saline-injected group even on 14 d.p.i. H-1 virions were also detected in the damaged tumor cells with numerous vacuoles in cytoplasm. Specific band (908 bp) of H-1 DNA and ABC immunostaining indicated H-1 DNA replication and NS-1 expression in tumors of treated groups, their time course was well in accordance with that process of necrosis. These results suggest that parvovirus H-1 promotes tumor necrosis by its DNA replication and cytotoxic NS-1 protein expression, and thus, it inhibits hepatoma growth and induces oncosuppression and oncolysis.

Animals↗

Inhibition of poly(ADP-ribose) polymerase increases (+/-)-anti-benzo [a]pyrene diolepoxide-induced micronuclei formation and p53 accumulation in isolated human peripheral blood lymphocytes.

In response to DNA damage, in particular DNA strand breaks, the proposed roles for normal tumour suppressor protein p53 are to increase the period of time available for DNA repair prior to replication, or to direct damaged cells into programmed cell-death. Since treatment of mammalian cells with (+/-)-anti-benzo[a]pyrene diolepoxide [(+/-)-anti-BPDE] --a mixture of metabolites comprising the most reactive (+)-anti-enantiomer of the full environmental carcinogen benzo[a]pyrene--has been shown to result in induction of DNA repair processes and consequently in DNA strand break formation, the aim of the present study was to investigate whether p53 accumulation is induced in (+/-)-anti-BPDE-treated phytohaemagglutinin-stimulated human peripheral blood lymphocytes (PBLs). Both immunocytochemical and immunoblot analysis indicated that treatment of PBLs with (+/-)-anti-BPDE results in p53 accumulation. Optimal accumulation was observed at 2.5 microM, while no increase of p53 levels was observed at concentrations < 2.5 microM and > 10 microM. Further, (+/-)-anti-BPDE-induced p53 accumulation in PBLs was found to be time-dependent with accumulation up to 24 h after the onset of treatment. Treatment of PBLs with 2.5 microM of (+/-)-anti-BPDE and 1 mM of 3-aminobenzamide, an inhibitor of the DNA strand break-dependent enzyme poly(ADP-ribose) polymerase, resulted in increased p53 levels, in comparison to cells treated with (+/-)-anti-BPDE alone. This combination also potentiated the frequency of (+/-)-anti-BPDE-induced micronuclei. These findings suggest that (+/-)-anti-BPDE-induced DNA strand break formation is responsible for the observed p53 accumulation. It is unlikely that poly(ADP-ribose) polymer formation is a prerequisite in the process of p53 accumulation, as triggered by DNA strand-break inducing agents like (+/-)-anti-BPDE. It is hypothesized that p53-dependent pathways may be activated in phytohaemagglutinin-stimulated human peripheral blood lymphocytes exposed ex vivo to (+/-)-anti-BPDE.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

Preferential replication of repeated DNA sequences in nuclei isolated from soybean cells grown in suspension culture.

Nuclei isolated from suspension cultures of soybean cells are able to replicate DNA in vitro for short periods of time. The reaction is not blocked by dideoxythymidine triphosphate, suggesting that DNA polymerase alpha is involved. Reassociation kinetics, restriction analysis, and isopycnic centrifugation of the DNA synthesized in vitro show that repeated sequences are preferentially replicated in isolated nuclei. However, some repeated sequences are not replicated in vitro, including those coding for ribosomal RNA. The addition of cytoplasmic or yeast extracts clearly stimulates DNA replication in vitro but does not improve the ability of nuclei to replicate single copy DNA. Incubation of cells with cytokinins prior to the isolation of nuclei modifies the pattern of replication of repeated sequences in vitro. These experiments suggest that the replication of single copy and repeated nuclear sequences have different requirements and may be controlled in a different way in plant cells.

Cells, Cultured↗

The IE2 60-kilodalton and 40-kilodalton proteins are dispensable for human cytomegalovirus replication but are required for efficient delayed early and late gene expression and production of infectious virus.

The human cytomegalovirus (HCMV) IE2 86-kDa protein is an essential transactivator of viral and cellular gene expression. Additional proteins of 60 and 40 kDa are expressed from the IE2 gene at late times postinfection and are identical to the C terminus of IE2 86. We have constructed HCMV recombinants that express wild-type full-length IE2 86 but do not express the IE2 40- and 60-kDa proteins. Each of these recombinants is viable, indicating that neither the 60-kDa nor the 40-kDa protein is required for virus replication, either alone or in combination. Cells infected with the IE2 60 and IE2 40 deletion mutants, however, exhibit decreased expression of selected viral genes at late times. In particular, expression of the viral DNA replication factor UL84 is affected by the deletion of IE2 40, and expression of the tegument protein pp65 (ppUL83) is affected by the deletion of both IE2 40 and IE2 60. IE2 60 and IE2 40 are also required for the production of normal levels of infectious virus. Finally, IE2 40 appears to function as a repressor of major immediate-early transcription in the infected cell. These results begin to define functions for the IE2 60- and IE2 40-kDa proteins and indicate that these products contribute both to the expression of selected viral genes and to the overall progression of the infection.

Cytomegalovirus↗

[Residual DNA damages in irradiated HeLa cells].

A possibility to detect the low level residual DNA damages was undertaken in HeLa cells during a long time after irradiation. The mixture of two inhibitors of replicative and reparative syntheses (hydroxyurea and beta-arabinosylcytosine) was added to the HeLa monolayer culture cells 6--24 hours after irradiation, when the potentially lethal damages was removed. A decrease in cell survival was shown. These data suggest that a certain amount of damages may still remain in DNA of irradiated cells.

Cell Survival↗

Preferential association of newly synthesized histones with replicating SV40 DNA.

The assembly of newly synthesized histones into nucleosomes during replication of SV40 minichromosomes in vivo was studied. Infected cells were labeled with 35S-methionine for a time shorter than that required to complete a round of viral DNA replication. Mature and replicating SV40 minichromosomes were extracted and separated by zonal sedimentation, and their histone content was analyzed by polyacrylamide gel electrophoresis (SDS and acidic urea). We show that the pulse-labeled histones associate preferentially with the replicating DNA.

Cell Line↗

The regulation of the cell cycle during Drosophila embryogenesis: the transition to polyteny.

The process of polytenization plays a crucial role in Drosophila development, and most of the larval tissues are polytene. By analyzing the pattern of DNA replication in embryos pulse-labeled with BrdU, we show that many larval tissues undergo a transition to begin becoming polytene late in embryogenesis. Our results demonstrate that in these larval tissues polyteny results from a modified cell cycle, the endo cell cycle, in which there is only an S (synthesis) phase and a G (gap) phase. A key regulator of the mitotic cell cycle, the product of the string gene (the Drosophila homologue of cdc25), is not required for the endo cell cycle. The developmental regulation of the endo cell cycle is striking in that tissue-specific domains undergo polytene DNA replication in a dynamic pattern at defined times in embryogenesis. During subsequent rounds of the endo cell cycle in late embryogenesis and first instar larval development, the domains are subdivided and the temporal control is not as rigid. The length of the G phase varies among different tissues. By quantifying DNA content, we show that during the early polytene S phases the genome is not fully duplicated.

Animals↗

Adenovirus homologous recombination does not require expression of the immediate-early E1a gene.

To investigate whether early genes other than those involved directly in DNA replication are required for efficient adenovirus recombination, pairs of viruses with deletions in E1a, E1b 496R, E1b 196R, or E4 and containing differing restriction site markers were used to infect both permissive and non- or semipermissive cells. Recombination was assayed among intracellular and extracellular genomes by restriction digestion and blot hybridization. Recombination was delayed in infections of nonpermissive cells with E1a- viruses until a time consistent with the late onset of DNA replication characteristic of the cell type. This shows that E1a expression is not absolutely required for adenovirus recombination. Similar tests with deletion mutations in E1b and E4 also show that these genes are not required for efficient recombination. Taken together with earlier results showing that recombination depends on DNA replication, it is likely that adenovirus recombination is a consequence of cellular repair functions acting on the substrates produced by replication.

Adenoviridae↗

Sodium butyrate stimulates DNA repair in UV-irradiated normal and xeroderma pigmentosum human fibroblasts.

Histone acetylation, DNA replicative synthesis, UV-induced DNA repair synthesis, and UV-induced endonuclease-sensitive sites were measured in normal human fibroblasts and xeroderma pigmentosum fibroblasts (complementation groups A, C, and D) following exposure to sodium butyrate. In all four cell types, treatment with millimolar concentrations of sodium butyrate resulted in a hyperacetylation of the core histones. Furthermore, following an exposure of 20 mM sodium butyrate for 48 h, the extent of hyperacetylation was the same in each cell type. In agreement with previous reports, we observed a marked decrease in DNA replicative synthesis in each cell type following increasing times of exposure to sodium butyrate. On the other hand, we observed a marked increase in DNA repair synthesis occurring during early times after UV irradiation in normal cells and in two of the xeroderma pigmentosum cell strains (groups C and D). This increase appeared to correlate with the increase in the highest acetylated form of histone H4. Furthermore, the total number of endonuclease-sensitive sites (i.e. prior to the onset of repair) induced by UV radiation was the same in both butyrated-treated and untreated normal cells over the dose range of 0-20 J/m2. However, the initial rate of removal of these sites increased in butyrate-treated normal cells. These results indicate that sodium butyrate stimulates the initial rate of nucleotide excision repair in both normal and (partially) repair-deficient human cells at concentrations where the histones are maximally hyperacetylated.

Butyrates↗