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Initiation of DNA replication in nuclei from quiescent cells requires permeabilization of the nuclear membrane.

We have investigated the replication capacity of intact nuclei from quiescent cells using Xenopus egg extract. Nuclei, with intact nuclear membranes, were isolated from both exponentially growing and contact-inhibited BALB/c 3T3 fibroblasts by treatment of the cells with streptolysin-O. Flow cytometry showed that > 90% of all contact-inhibited cells and approximately 50% of the exponential cells were in G0/G1-phase at the time of nuclear isolation. Intact nuclei were assayed for replication in the extract by incorporation of [alpha-32P]dATP or biotin-dUTP into nascent DNA. Most nuclei from exponential cells replicated in the egg extract, consistent with previous results showing that intact G1 nuclei from HeLa cells replicate in this system. In contrast, few nuclei from quiescent cells replicated in parallel incubations. However, when the nuclear membranes of these intact quiescent nuclei were permeabilized with lysophosphatidylcholine prior to addition to the extract, nearly all the nuclei replicated under complete cell cycle control in a subsequent incubation. The ability of LPC-treated quiescent nuclei to undergo DNA replication was reversed by resealing permeable nuclear membranes with Xenopus egg membranes prior to extract incubation demonstrating that the effect of LPC treatment is at the level of the nuclear membrane. These results indicate that nuclei from G1-phase cells lose their capacity to initiate DNA replication following density-dependent growth arrest and suggest that changes in nuclear membrane permeability may be required for the initiation of replication upon re-entry of the quiescent cell into the cell cycle.

3T3 Cells↗

Nuclear proteins of quiescent Xenopus laevis cells inhibit DNA replication in intact and permeabilized nuclei.

Quiescent cells from adult vertebrate liver and contact-inhibited or serum-deprived tissue cultures are active metabolically but do not carry out nuclear DNA replication and cell division. Replication of intact nuclei isolated from either quiescent Xenopus liver or cultured Xenopus A6 cells in quiescence was barely detectable in interphase extracts of Xenopus laevis eggs, although Xenopus sperm chromatin was replicated with approximately 100% efficiency in the same extracts. Permeabilization of nuclei from quiescent Xenopus liver or cultured Xenopus epithelial A6 cells did not facilitate efficient replication in egg extracts. Moreover, replication of Xenopus sperm chromatin in egg extracts was strongly inhibited by a soluble extract of isolated Xenopus liver nuclei; in contrast, complementary-strand synthesis on single-stranded DNA templates in egg extracts was not affected. Inhibition was specific to endogenous molecules localized preferentially in quiescent as opposed to proliferating cell nuclei, and was not due to suppression of cdk2 kinase activity. Extracts of Xenopus liver nuclei also inhibited growth of sperm nuclei formed in egg extracts. However, the rate and extent of decondensation of sperm chromatin in egg extracts were not affected. The formation of prereplication centers detected by anti-RP-A antibody was not affected by extracts of liver nuclei, but formation of active replication foci was blocked by the same extracts. Inhibition of DNA replication was alleviated when liver nuclear extracts were added to metaphase egg extracts before or immediately after Ca++ ion-induced transition to interphase. A plausible interpretation of our data is that endogenous inhibitors of DNA replication play an important role in establishing and maintaining a quiescent state in Xenopus cells, both in vivo and in cultured cells, perhaps by negatively regulating positive modulators of the replication machinery.

Animals↗

Dynamics of DNA replication factories in living cells.

DNA replication occurs in microscopically visible complexes at discrete sites (replication foci) in the nucleus. These foci consist of DNA associated with replication machineries, i.e., large protein complexes involved in DNA replication. To study the dynamics of these nuclear replication foci in living cells, we fused proliferating cell nuclear antigen (PCNA), a central component of the replication machinery, with the green fluorescent protein (GFP). Imaging of stable cell lines expressing low levels of GFP-PCNA showed that replication foci are heterogeneous in size and lifetime. Time-lapse studies revealed that replication foci clearly differ from nuclear speckles and coiled bodies as they neither show directional movements, nor do they seem to merge or divide. These four dimensional analyses suggested that replication factories are stably anchored in the nucleus and that changes in the pattern occur through gradual, coordinated, but asynchronous, assembly and disassembly throughout S phase.

Animals↗

Inhibition of HIV replication and macrophage colony-stimulating factor production in human macrophages by antiretroviral agents.

Macrophage colony-stimulating factor (M-CSF) enhances the susceptibility of macrophages to infection with HIV-1, in part by increasing the expression of CD4 and CCR5. Human monocyte-derived macrophages (MDMs) infected in vitro with HIV-1 endogenously produce M-CSF, with kinetics paralleling virus replication, which can lead to enhanced spreading of the infection. AZT and ritonavir both inhibit HIV replication, but their impact on M-CSF production by HIV-infected human MDMs is unknown. The dose response and kinetics of virus replication in the presence of AZT and ritonavir were determined for HIV-infected MDMs from HIV-seronegative donors. Harvested supernatants were monitored for reverse transcriptase activity, M-CSF production, and HIV proteins. Our data suggest that threshold levels of HIV replication must occur before maximum M-CSF production is induced. Addition of AZT or ritonavir before or after establishment of productive HIV infection dramatically reduces virus replication and M-CSF production by human MDMs. However, ongoing virus replication and M-CSF production are slow to return to baseline levels after addition of AZT or ritonavir, suggesting that HIV replication and virion release from infected macrophages continue long after initiation of antiretroviral therapy. Our results suggest that, in human macrophages, HIV-1 replication and M-CSF production are inextricably linked, such that inhibition of one leads to a concomitant reduction of the other. Low-level HIV replication and M-CSF release during ongoing antiretroviral therapies may facilitate the survival and maintenance of infected macrophages and suggests that additional therapies targeting M-CSF may be critical for elimination of macrophage reservoirs.

Anti-HIV Agents↗

TAR- and Tat-independent replication of human immunodeficiency virus type 1 in human hepatoma cells.

The molecular mechanisms involved in the regulation of human immunodeficiency virus type 1 (HIV-1) replication may differ in various cell types and with various exogenous stimuli. TAR/Tat interactions play important roles in HIV-1-long terminal repeat (LTR)-directed transcription, and have become specific targets in molecular therapies for blocking HIV-1 replication. As we previously reported, astrocytic glial cells, which can support HIV-1 replication in cell culture and may be infected in vivo, provide an intracellular milieu in which TAR mutant HIV-1 viruses may replicate. In further studies of this molecular model, several divergent human cell types were analyzed for both TAR- and Tat-independent HIV-1 replication. Human hepatoma cell lines, which can be productively infected by HIV-1 after the hepatoma cells are transduced with the human CD4 receptor gene, were found to support high levels of HIV-1 replication. In these studies, utilizing a transient transfection system with wild-type and various TAR, Tat, or combined TAR/Tat mutant HIV-1 proviral constructs, we demonstrate TAR-independent replication in unstimulated human hepatoma cells. Remarkably, in human hepatoma cells, HIV-1 replication is not only independent of TAR but also can be independent of Tat expression. It is further demonstrated, using electrophoretic mobility shift assays (EMSAs) and an in situ UV cross-linking system, that human hepatoma cells contain novel endogenous cellular proteins that bind to the proviral HIV-1 5' LTR in the downstream region, between nucleotides +38 to +125 on proviral DNA. This alternative regulatory pathway of TAR- and Tat-independent viral production may provide a new system to dissect further the interactions of Tat/TAR and determine the role of the TAR element, in its DNA form, in HIV-1 replication.

Base Sequence↗

A method of limited replication for the efficient in vivo delivery of adenovirus to cancer cells.

Replication-deficient viral vectors are currently being used in gene transfer strategies to treat cancer cells. Unfortunately, viruses are limited in their ability to diffuse through tissue. This makes it virtually impossible to infect the majority of tumor cells in vivo and results in inadequate gene transfer. This problem can be addressed by allowing limited viral replication. Limited viral replication facilitates greater penetration of virions into tissue and can improve gene transfer. We have developed a strategy of limited viral replication using AdRSVlaclys, a chemically modified E1-deleted adenovirus, to codeliver an exogenous plasmid encoding the adenovirus E1 region. This system allows one round of viral replication. We examined the effect of this limited adenovirus replication in vitro and in vivo. In culture, codelivery of virus and pE1 resulted in a large increase in infected cells when compared with control cells exposed to virus and pUC19. In experiments on nude mice bearing HeLa ascites tumors, intraperitoneal injection of AdRSVlaclys/pE1 resulted in a significantly higher percentage of infected HeLa cells as compared with the PBS controls (p < 0.05) or the AdRSVlaclys/pUC19 controls (p < 0.01). These data demonstrate that the transcomplementation of replication-deficient adenovirus with exogenous E1 DNA leads to limited replication, and this controlled replication enhances gene transfer efficiency of adenovirus in vivo.

Adenoviridae↗

Etoposide induces the dispersal of DNA ligase I from replication factories.

In eukaryotic cells DNA replication occurs in specific nuclear compartments, called replication factories, that undergo complex rearrangements during S-phase. The molecular mechanisms underlying the dynamics of replication factories are still poorly defined. Here we show that etoposide, an anticancer drug that induces double-strand breaks, triggers the redistribution of DNA ligase I and proliferating cell nuclear antigen from replicative patterns and the ensuing dephosphorylation of DNA ligase I. Moreover, etoposide triggers the formation of RPA foci, distinct from replication factories. The effect of etoposide on DNA ligase I localization is prevented by aphidicolin, an inhibitor of DNA replication, and by staurosporine, a protein kinase inhibitor and checkpoints' abrogator. We suggest that dispersal of DNA ligase I is triggered by an intra-S-phase checkpoint activated when replicative forks meet topoisomerase II-DNA--cleavable complexes. However, etoposide treatment of ataxia telangiectasia cells demonstrated that ataxia-telangiectasia-mutated activity is not required for the disassembly of replication factories and the formation of replication protein A foci.

Antineoplastic Agents, Phytogenic↗

Relationship between composition of lymphoid cell infiltrates in the liver and replication status in chronic hepatitis B: an immunohistochemical study.

The purpose of this in situ immunophenotyping study was to assess the nature of lymphoid cells involved in chronic hepatitis B with various levels of replication. Replicative status was studied in 25 patients with chronic hepatitis B. Different subsets of T cells, B cells, natural killer cells, and follicular dendritic cells were counted with a computerized image analyzer. Twelve patients had chronic hepatitis B with a high level of replication, nine without replication, and four with a low level of replication. The number of CD3+ T cells was significantly higher in the liver of patients with replication. In all cases, CD8+ T cells were the most numerous cells in the lobules and CD4+ T cells were the most numerous cells in the portal tract. Intra-portal lymphoid follicles were observed in 33% of patients with a high level of replication. The CD57+ natural killer cells were more numerous in patients with a low level of replication. This study suggests that in immunocompetent patients, the intensity and type of hepatic immune response are directly determined by the HBV replication.

Adult↗

DNA damage responses and their many interactions with the replication fork.

The cellular response to DNA damage is composed of cell cycle checkpoint and DNA repair mechanisms that serve to ensure proper replication of the genome prior to cell division. The function of the DNA damage response during DNA replication in S-phase is critical to this process. Recent evidence has suggested a number of interrelationships of DNA replication and cellular DNA damage responses. These include S-phase checkpoints which suppress replication initiation or elongation in response to DNA damage. Also, many components of the DNA damage response are required either for the stabilization of, or for restarting, stalled replication forks. Further, translesion synthesis permits DNA replication to proceed in the presence of DNA damage and can be coordinated with subsequent repair by homologous recombination (HR). Finally, cohesion of sister chromatids is established coincident with DNA replication and is required for subsequent DNA repair by homologous recombination. Here we review these processes, all of which occur at, or are related to, the advancing replication fork. We speculate that these multiple interdependencies of DNA replication and DNA damage responses integrate the many steps necessary to ensure accurate duplication of the genome.

Animals↗

Regulation of replication timing in fission yeast.

Here we report the first characterization of replication timing and its regulation in the fission yeast Schizosaccharomyces pombe. We used three different synchronization methods: centrifugal elutriation, cdc10 temperature-shift and release, and starvation for deoxyribonucleoside triphosphates (dNTPs) by treatment with hydroxyurea (HU) followed by removal of HU, to study the times when specific autonomously replicating sequence elements (ARS elements; potential replication origins) replicate during S phase. We found that individual ARS elements replicate at characteristic times, some early and some late, independently of synchronization method. In wild-type cells treated with HU, early ARS elements replicated but late ones did not. However, in HU-treated mutant cells lacking the Rad3 (similar to human ATR and ATM) or Cds1 (similar to human CHK2) checkpoint kinase, both early and late ARS elements were able to replicate. Thus under conditions of dNTP starvation the Rad3 and Cds1 kinases are needed to suppress the replication of normally late-replicating regions.

Adenosine Triphosphatases↗

Identification of genomic regions required for DNA replication during Drosophila embryogenesis.

A collection of Drosophila deficiency stocks was examined by bromodeoxyuridine (BrdU) labeling of embryos to analyze the DNA replication patterns in late embryogenesis. This permitted us to screen 34% of the genome for genes that when absent in homozygous deficiencies affect the cell cycle or DNA replication. We found three genomic intervals that when deleted result in cessation of DNA replication in the embryo, 39D2-3;E2-F1, 51E and 75C5-7;F1. Embryos deleted for the 75C5-7;F1 region stop DNA replication at the time in embryogenesis when a G1 phase is added to the mitotic cell cycle and the larval tissues begin to become polytene. Thus, this interval may contain a gene controlling these cell cycle transitions. DNA replication arrests earlier in embryos homozygous for deletions for the other two regions. Analysis of the effects of deletions in the 39D2-3;E2-F1 region on DNA replication showed that the block to DNA replication correlates with deletion of the histone genes. We were able to identify a single, lethal complementation group in 51E, l(2)51Ec, that is responsible for the cessation of replication observed in this interval. Deficiencies that removed one of the Drosophila cdc2 genes and the cyclin A gene had no effect on replication during embryogenesis. Additionally, our analysis identified a gene, pimples, that is required for the proper completion of mitosis in the post-blastoderm divisions of the embryo.

Animals↗

Coupling of Saccharomyces cerevisiae early meiotic gene expression to DNA replication depends upon RPD3 and SIN3.

It has been established that meiotic recombination and chromosome segregation are inhibited when meiotic DNA replication is blocked. Here we demonstrate that early meiotic gene (EMG) expression is also inhibited by a block in replication. Since early meiotic genes are required to promote meiotic recombination and DNA division, the low expression of these genes may contribute to the block in meiotic progression. We have identified three Hur- (HU reduced recombination) mutants that fail to couple meiotic recombination and gene expression with replication. One of these mutations is in RPD3, a gene required to maintain meiotic gene repression in mitotic cells. Complete deletions of RPD3 and the repression adapter SIN3 permitted recombination and early meiotic gene expression when replication was inhibited with hydroxyurea (HU). Biochemical analysis showed that the Rpd3p-Sin3p-Ume6p repression complex does exist in meiotic cells. These observations suggest that repression of early meiotic genes by SIN3 and RPD3 is critical for the normal response to inhibited replication. A second response to inhibited replication has also been discovered. HU-inhibited replication reduced the accumulation of phospho-Ume6p in meiotic cells. Phosphorylation of Ume6p normally promotes interaction with the meiotic activator Ime1p, thereby activating EMG expression. Thus, inhibited replication may also reduce the Ume6p-dependent activation of EMGs. Taken together, our data suggest that both active repression and reduced activation combine to inhibit EMG expression when replication is inhibited.

Blotting, Northern↗

Sister chromatid exchanges in cells defective in mismatch, post-replication and excision repair.

Three processes associated with DNA damage and genomic instability have been defined experimentally as operating during or soon after DNA replication: mismatch repair, post-replication repair and sister chromatid exchange. All these processes appear to operate on damage and/or errors in newly replicated DNA. Both mismatch repair and post-replication repair involve resynthesis of up to 1 kb of newly synthesized DNA: mismatch repair operates on single-base or slippage errors; post-replication repair operates on persistent gaps in newly synthesized DNA caused by damage on parental strands. Using colon cancer cells with different mismatch repair capacity, together with normal cells and excision-repair-defective and post-replication-repair-defective xeroderma pigmentosum (XP) cells, we analysed possible interactions between these processes. No evidence for overlap of mismatch repair with excision or post-replication repair was found. However, post-replication-repair-defective XP variant cells that were SV40 transformed showed higher UV-induced sister chromatid exchange frequencies than did untransformed cells. This suggests that sister chromatid exchanges in the XP variant are closely involved with UV-induced replication errors that are enhanced by transformation.

Caffeine↗

Sequences that promote formation of catenated intertwines during termination of DNA replication.

The normal sequence at which SV40 DNA replication terminates (TER) is unusual in that it promotes formation of catenated intertwines when two converging replication forks enter to complete replication (Weaver et al., 1985). Here we show that yeast centromeric sequences also exhibit this phenomenon. CEN3 caused accumulation of late replicating intermediates and catenated dimers in plasmids replicating in mammalian cells, but only when it was located in the termination region (180 degrees from ori), and only when cells were subjected to hypertonic shock to reduce topoisomerase II activity. Therefore, formation of catenated intertwines during termination of DNA replication was sequence dependent, suggesting that topoisomerase II acts behind replication forks in the termination region to remove intertwines generated by unwinding DNA rather than acting after replication is completed and catenates are formed. Under normal physiological conditions, CEN3 did not promote formation of catenated dimers in either mammalian or yeast cells. Therefore, CEN does not maintain association of sister chromatids during mitosis in yeast by introducing stable catenated intertwines during replication.

Cell Cycle↗

Replication fork barriers in the Xenopus rDNA.

To investigate replication fork progression along the tandemly repeated rRNA genes of Xenopus laevis and Xenopus borealis, rDNA replication intermediates from dividing tissue culture cells were analyzed by two-dimensional gel electrophoresis. Analysis of the direction of replication in the rRNA coding regions revealed replication forks moving in both directions. However, in both frog species, polar replication fork barriers (RFB) arresting forks approaching the rRNA transcription units from downstream were identified. Whereas in X. borealis the RFB maps to a defined site close to the transcription terminator, in X. laevis the arrest of fork movement can occur at multiple positions throughout a 3' flanking repetitive spacer region. A short DNA element located near the respective RFB sites is shared between these two related frog species, suggesting its possible involvement in the arrest of replication fork movement. In a subset of rDNA repeats, these barriers cause an absolute block to replication fork progression, defining the sites where replicon fusion occurs, whereas in the remainder repeats, most probably in the non-transcribed gene copies, the replication machinery can pass the RFB sequences and replicate the rRNA transcription unit in a 3'-to-5' direction.

Animals↗

RANTES, MIP-1 alpha and MIP-1 beta are not involved in the inhibition of HIV-1SF33 replication mediated by CD8+ T-cell clones.

OBJECTIVE: To determine whether CD8+ cells inhibit HIV replication in vitro through the chemokines RANTES, macrophage inflammatory protein (MIP)-1 alpha and MIP-1 beta. DESIGN AND METHODS: CD8+ T-cell clones were screened for their ability to inhibit HIV-1SF33 replication in CD4+ cells using p24 antigen and HIV RNA levels as endpoints. It has been suggested that such inhibition is mediated by three type cc chemokines: RANTES, MIP-1 alpha and MIP-1 beta. To assess whether our T-cell clones inhibited HIV replication through a similar mechanism, the clones' ability to inhibit HIV-1SF33 replication was compared with their secretion of RANTES, MIP-1 alpha and MIP-1 beta. Moreover, we tested the effects of neutralizing antibodies (NAb) against these factors on the anti HIV-1SF33 activity of our clones as well as the direct effect of these recombinant cc-chemokines on HIV-1SF33 replication. RESULTS: The CD8+ T-cell clone; tested differed by their capacity to inhibit HIV-1 replication. We showed no correlation between the ability of these clones to secrete RANTES, MIP-1 alpha and MIP-1 beta and their ability to repress HIV-1SF33 replication. In addition, this inhibitory activity against HIV-1SF33 could not be blocked by NAb directed against these chemokines, nor could these chemokines significantly inhibit HIV-1SF33 replication in acutely infected CD4+ cells in vitro. CONCLUSION: The data indicate that CD8+ cells can inhibit HIV-1SF33 replication in vitro by mechanisms that do not involve either cytotoxicity or RANTES, MIP-1 alpha and MIP-1 beta.

Antibodies↗

Granulocyte-macrophage colony-stimulating factor inhibits HIV-1 replication in monocyte-derived macrophages.

BACKGROUND: Previous studies of the effect of granulocyte-macrophage colony-stimulating factor (GM-CSF) on HIV-1 replication in macrophages have had inconsistent results, variously reporting no effect, augmentation or inhibition of viral replication. OBJECTIVE: To investigate the regulation of HIV-1 in monocyte-derived macrophages (MDM) by GM-CSF in vitro. METHODS: The role of GM-CSF on HIV-1 replication was assessed as supernatant and intracellular p24 antigen concentrations and by HIV-1 DNA and mRNA production under different culture conditions. Expression of CD4 and CCR5 receptors was examined. The effect of GM-CSF with an E21R mutation, which binds only to the alpha-chain of GM-CSF receptor, was used as an additional control. RESULTS: GM-CSF consistently suppressed HIV-1 replication in human MDM in vitro, as assessed by supernatant and intracellular p24 antigen concentrations and HIV-1 gag mRNA expression. The inhibitory effect of GM-CSF on HIV-1 replication was observed regardless of HIV-1 strain, source of GM-CSF, stage of MDM maturation or timing of GM-CSF exposure in relation to HIV-1 infection. The effect was dose dependent and reversed by addition of a neutralizing monoclonal antibody (4D4). Flow cytometric analysis of surface expression of CD4 and CCR5 indicates that GM-CSF does not affect HIV-1 entry into MDM. Analysis of intracellular HIV-1 DNA and mRNA suggests that HIV-1 replication is inhibited at or before transcription. E21R GM-CSF had no effect on HIV-1 replication in MDM. CONCLUSIONS: GM-CSF regulates HIV-1 replication in MDM, inhibiting HIV-1 replication through binding to the beta-chain of the GM-CSF receptor.

Cells, Cultured↗

Asynchronous replication of biallelically expressed loci: a new phenomenon in Turner syndrome.

PURPOSE: Transcriptional activity of genes is related to their replication timing; alleles showing the common biallelic mode of expression replicate synchronously, whereas those with a monoallelic mode of expression replicate asynchronously. Here the level of synchronization in replication timing of alleles was determined in subjects with Turner syndrome. METHODS: Fluorescence in situ hybridization was used for three loci not linked to X chromosome, in lymphocytes derived from 12 controls, 3 individuals with Turner, and 4 with mosaic Turner syndrome. RESULTS: In cells derived from controls, each pair of alleles replicated synchronously; yet these same alleles replicated asynchronously in cells monosomic for X chromosome derived from Turner and mosaic Turner patients. When the level of 45,X was low in the mosaic samples, the replication pattern of the 46,XX cells was normal. However, in samples with a high level of mosaicism, a significantly increased asynchronous replication was detected in the 46,XX cells. CONCLUSION: An altered temporal replication control in Turner syndrome affecting the aneuploid and euploid cells is shown. This alteration may potentially be involved in the determination of the syndrome.

Alleles↗