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PubMed2000

In vitro replication and differentiation of normal human oral keratinocytes.

The replication kinetics and cytological changes of normal human oral keratinocytes (NHOK) isolated from the basal surface of oral epithelial sheet and cultured as dispersed cells in low (0.15 mM) Ca(2+) medium without serum were analyzed. Replicating NHOK were quantitated by cell count and identified by [(3)H]thymidine uptake. Cell morphology was analyzed by phase contrast and transmission electron microscopy, and by cytochemical staining for endogenous beta-galactosidase (beta-gal) activity, involucrin, and cytokeratin types 1 and 10 (K1/K10). Primary NHOK obtained from 15 different donors whose ages ranged from 21 to 62 years consistently showed three distinct phases of replication, i.e., exponential, senescing, and senescent, which were independent of the donors' age. Initially, the cells replicated exponentially for a period of 20 days with a doubling time of 26.6 +/- 3.5 h. They then gradually entered replication arrest over a period of 18 days. The cells underwent a maximum of 22.1 +/- 2.8 population doublings. The onset of gradual replication arrest coincided with an increase in the fraction of cells, which stopped DNA synthesis within a maximum of 48 h and which stained for beta-gal. The fraction of terminally differentiated cells stained for K1/K10 did not increase until nearly all the cells had stopped replicating (senescent phase) and maximal beta-gal staining had been reached. Subsequently, the percentage of beta-gal stained cells actually decreased while the percentage of those stained for K1/K10 increased to a maximum of 80-90% within 2-3 weeks. Exposure of exponentially replicating NHOK to 5-aza-2'-deoxycytidine (5-aza CdR) inhibited DNA replication within 18-48 h and induced terminal differentiation 6 days later. In contrast, exposure of these cells to 1.5 mM Ca(2+) induced expression of involucrin and K1/K10 within 48 h without inhibiting DNA synthesis. Thus, replication arrest preceded differentiation in NHOK serially subcultured in vitro; however, differentiation could be induced without replication arrest.

Adult↗
PubMed1993

Cis- and trans-acting elements in cowpea mosaic virus RNA replication.

Cowpea mosaic virus (CPMV) B-RNA encodes the viral proteins required for viral RNA replication while M-RNA does so for the capsid proteins and functions required in cell-to-cell movement of the virus. Accordingly, B-RNA can replicate by itself, whereas M-RNA can only replicate in the presence of B-RNA. We have made heterologous sequence insertions at different positions in the open reading frame of B-RNA, leaving the 5' and 3' non-coding ends intact. None of these mutant B-RNAs were able to replicate. Furthermore, it was not possible to support replication of these mutant B-RNAs by co-inoculating wild-type B-RNA as a helper, indicating that B-RNA can not be replicated in trans. In contrast, replication of M-RNA must occur in trans, as the viral replicative proteins are encoded by B-RNA. Mutant M-RNA transcripts containing 5' and 3' non-coding regions of B-RNA are still efficiently replicated in protoplasts if co-inoculated with B-RNA, indicating that in cis or in trans replication of the CPMV RNAs is not primarily determined by the non-coding regions. Remarkably, for replication of M-RNA, the N-terminal domain of the 58K protein encoded by M-RNA was found to be required.

Base Sequence↗
PubMed1997

Genome nucleotide lengths that are divisible by six are not essential but enhance replication of defective interfering RNAs of the paramyxovirus simian virus 5.

For some members of the Paramyxoviridae family of negative strand RNA viruses, efficient genome replication only occurs when the total genome length is a multiple of six (6N length, where N is any integer). To determine if this "rule of six" requirement applied to the replication of the prototype paramyxovirus simian virus 5 (SV5), defective interfering (DI) RNA genomes were generated by sequential undiluted passage of virus in tissue culture. Molecular cloning and nucleotide sequence analysis of 10 RNA genomes revealed a series of copyback DI RNAs with chain lengths between 449 and 1365 bases, but only 4 of the 10 naturally occurring RNA genomes were of 6N length. Many of the cloned DI genomes could be grouped into two distinct nested sets, with the members of each set having the same polymerase crossover junctions and extent of terminal complementarity but differing from each other by internal deletions. One of these nested sets of genomes consisted of novel DI RNAs that contained a pentameric stretch of nontemplated adenosine residues inserted precisely at the polymerase crossover junction. A reverse genetics system was established in which SV5 DI genomes were replicated in vivo entirely by cDNA-derived components. Using this system, two naturally occurring SV5 DI RNAs were examined in a mutational analysis to determine the role of genome length on SV5 RNA replication. The progressive insertion of one to six nucleotides into a 6N length DI genome (852 bases) resulted in a reduction in replication for RNAs that contained one to four additional bases (approximately 35-50% of WT levels), followed by an increase back to WT replication levels for genomes that were altered by five and six base insertions (approximately 70 and 100% of WT levels, respectively). An insertion of five nucleotides into a second non-6N length DI RNA (499 total bases) created a genome length that was a multiple of six (504 bases) and led to a approximately 10-fold stimulation of replication over that of the unaltered genome. Together, these results indicate that there was a clear influence of 6N genome length on SV5 DI RNA replication, but the stringency of this replication requirement appeared to be less than that found previously for other paramyxoviruses. This work completes the testing of the rule of six replication requirement for representatives of each of the four genera of the Paramyxoviridae family and indicates that the preference for replication of 6N length RNA genomes varies between the individual paramyxoviruses.

Animals↗
PubMed1997

Undectable expression of hMLH1 protein in sporadic colorectal cancer with replication error phenotype.

PURPOSE: Four DNA mismatch repair genes have been identified as being susceptible genes for hereditary nonpolyposis colorectal cancer. Deficiency of one of the mismatch repair genes causes the replication error phenotype in more than 80 percent of patients with hereditary nonpolyposis colorectal cancer and in 10 to 30 percent of patients with sporadic colorectal cancer. To determine which mismatch repair gene is lacking the function in patients with replication error-positive colorectal cancer, several approaches have been used at the nucleic acid and protein levels. We studied replication error in 40 samples of randomly selected colorectal cancers and expression of hMSH2 and hMLH1 proteins analyzed by immunoblot in the tumor and normal tissues of the replication error-positive and replication error-negative samples. MATERIALS AND METHODS: Frozen tumor and normal tissues were obtained from 40 Japanese patients who had colorectal cancer. According to the Amsterdam criteria, those patients were classified as having 39 sporadic and 1 unknown colorectal cancers. Genomic DNA was extracted from tumor and normal tissues for determining replication error with eight microsatellite markers. Expression of hMSH2 and hMLH1 proteins in cell lysates of tumor and normal tissues of 16 patients was analyzed by immunoblot. RESULTS: The replication error phenotype was found in 6 (15 percent) of the 39 sporadic cases. hMLH1 protein was not detected in two of the six replication error-positive tumor tissues and not in the normal tissues, indicating that the tumor cells of the two patients had severe mutations in both alleles of the hMLH1 gene. Another four replication error-positive and ten replication error-negative tumors and normal tissues expressed hMLH1 protein. hMSH2 protein was detected in all samples. CONCLUSION: hMLH1 protein was undetectable in the two tumor tissues of the six replication error-positive samples of sporadic colorectal cancer. The detection procedure used here may have potential use for determining a dysfunctional mismatch repair gene product.

Adaptor Proteins, Signal Transducing↗
PubMed1998

The significance of precisely replicating patterns in mammalian CNS spike trains.

Neuronal spike trains from both single and multi-unit recordings often contain patterns such as doublets and triplets of spikes that precisely replicate themselves at a later time. The presence of such precisely replicating patterns can still be detected when the tolerance on interval replication is shortened to a fraction of a millisecond. In this context we examine here data taken from various parts of the central nervous systems of anesthetized rats, cats and monkeys. The relative abundance of replicating triplets varies from centre to centre, and is nearly always significantly greater than obtained in Monte-Carlo simulations of either a Poisson-like process or a renewal process having the same interspike interval distribution as the neuronal data. However, a remarkable exception is found in the activity of retinal ganglion cells. Significant deviations were found in the primary visual cortex and, even more so, in the lateral geniculate body and the mitral cells of the olfactory bulb. Using a fixed tolerance for the replication of intervals (0.5 ms) it is usually observed that replicating patterns are produced in excess (with respect to renewal process models) mostly in low firing rate episodes (< or = 100 Hz). However, using a tolerance that varies in direct proportion to the mean interval (i.e. as the reciprocal of the firing rate), one generally observes that replicating triplets occur with higher than expected frequency in comparable proportions at all firing rates. This observation suggests the existence of a scale invariance principle in these phenomena with respect to certain neuronal codes. In order to decrease the influence of the estimated neuronal firing rate on the results of the comparisons, we computed also the ratio NT2/ND3, of the number of replicating triplets to the number of doublets replicating three times [Lestienne R. (1994) Proc. Soc. Neurosci. 20, 22; Lestienne R. (1996) Biol. Cybern. 74, 55-61], using both a fixed or a variable tolerance. In spike trains obeying a Poisson process, NT2/ND3 ratios should be nearly independent of the frequency, especially when using a variable tolerance. These studies supported previous results: significant deviations from the models are found in all the spike trains examined, except in the case of retinal ganglion cells, and the most significant deviations are found in recordings from the lateral geniculate nucleus and the mitral cells of the olfactory bulb. Removing spikes that belong to bursts having large "Poisson surprise" values [Legéndy C. R. and Salcman M. (1985) J. Neurophysiol. 53, 926-939] (except the very first spike of the burst) significantly decreases NT2/ND3 ratios in the record from the lateral geniculate nucleus, suggesting that in this case bursty episodes greatly contribute to the production of replicating patterns, but such a removal does not affect results from the piriform record. Finally, in both the lateral geniculate nucleus and in the mitral cells of the olfactory bulb records, perturbing the timing of spikes by applying to interspike intervals small jitters of uniform probability density with amplitude up to 3 ms, very significantly decrease NT2/ND3 ratios in these centres, but does not change much the NT2/ND3 ratios in other neuronal recordings. Implications of these findings for a possible role of precisely replicating patterns in temporal coding of neuronal information is discussed, as well as possible mechanisms for their production.

Animals↗
PubMed2006

Optimal allocation of replicates for measurement evaluation studies.

Optimal experimental design is important for the efficient use of modern high-throughput technologies such as microarrays and proteomics. Multiple factors including the reliability of measurement system, which itself must be estimated from prior experimental work, could influence design decisions. In this study, we describe how the optimal number of replicate measures (technical replicates) for each biological sample (biological replicate) can be determined. Different allocations of biological and technical replicates were evaluated by minimizing the variance of the ratio of technical variance (measurement error) to the total variance (sum of sampling error and measurement error). We demonstrate that if the number of biological replicates and the number of technical replicates per biological sample are variable, while the total number of available measures is fixed, then the optimal allocation of replicates for measurement evaluation experiments requires two technical replicates for each biological replicate. Therefore, it is recommended to use two technical replicates for each biological replicate if the goal is to evaluate the reproducibility of measurements.

Computational Biology↗
PubMed2003

The role of DNA recombination in herpes simplex virus DNA replication.

In many organisms the processes of DNA replication and recombination are closely linked. For instance, in bacterial and eukaryotic systems, replication forks can become stalled or damaged, in many cases leading to the formation of double stranded breaks. Replication restart is an essential mechanism in which the recombination and repair machinery can be used to continue replication after such a catastrophic event. DNA viruses of bacteria such as lambda and T4 also rely heavily on DNA recombination to replicate their genomes and both viruses encode specialized gene products which are required for recombination-dependent replication. In this review, we examine the linkage between replication and recombination in the eukaryotic pathogen, Herpes Simplex Virus Type 1 (HSV-1). The evidence that recombination plays an intrinsic role in HSV-1 DNA replication and the infection process will be reviewed. We have recently demonstrated that HSV-1 encodes two proteins which may be analogous to the lambda phage recombination system, Red(alpha) and beta. The HSV-1 alkaline nuclease, a 5' to 3' exonuclease, and ICP8, a single stranded DNA binding protein, can carry out strand annealing reactions similar to those carried out by the lambda Red system. In addition, evidence suggesting that host recombination proteins may also be important for HSV-1 replication will be reviewed. In summary, it is likely that HSV-1 infection will require both viral and cellular proteins which participate in various pathways of recombination and that recombination-dependent replication is essential for the efficient replication of viral genomes.

Bacteria↗
PubMed2003

Same origins of DNA replication function on the active and inactive human X chromosomes.

We previously characterized a functional origin of DNA replication at the transcriptional promoter of the human hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene (Cohen et al. [2002] J. Cell. Biochem. 85:346-356). This origin was mapped using a quantitative PCR assay to evaluate the relative abundance of HPRT markers in short nascent DNA strands isolated from asynchronous cultures of male fibroblasts. The HPRT gene on the X chromosome is transcriptionally active in male human fibroblasts. It is known that on the heterochromatic X chromosome in female cells the HPRT gene is transcriptionally silenced and its replication timing changes from early to late in S phase. This change in replication timing could indicate that replication of the HPRT gene is under the control of different origins of DNA replication in the active (euchromatic, early replicating) and the inactive (heterochromatic, late replicating) X chromosomes. In the present study, we identified the location of the origin of replication of a second X chromosome gene, glucose-6-phosphate dehydrogenase (G6PD), which we mapped to its transcriptional promoter, in normal male human fibroblasts. Then, we determined the activity of the previously identified HPRT and the G6PD human origins in hybrid hamster cells carrying either the active or the inactive human X chromosome. The results of these studies clearly demonstrated that the human HPRT and G6PD origins of replication were utilized to the same extent in the active and the inactive X chromosomes. Therefore, transcription activity at the HPRT and G6PD genes is not necessary for initiation of DNA replication at the origins mapped to these chromosomal loci.

Animals↗
PubMed1998

Replication of R6K gamma origin in vitro: discrete start sites for DNA synthesis dependent on pi and its copy-up variants.

The regulation of the plasmid R6K gamma origin (gamma ori) is accomplished through the ability of the pi protein to act as an initiator and inhibitor of replication. Hyperactive variants of this protein, called copy-up pi, allow four to tenfold increases of gamma ori plasmid DNA in vivo. The higher activity of copy-up pi variants could be explained by an increase in the initiator function, a decrease in the inhibitor activity, or a derepression of a more efficient mechanism of replication that can be used by wt pi (pi35. 0) only under certain conditions. We have compared the replication activities of wt pi35.0 and copy-up pi mutants in vitro, and analyzed the replication products. It is shown that copy-up variants are several-fold more active than wt pi35.0 in replication. This appears to be due to enhanced specific replication activity of copy-up mutants rather than elevated fractions of protein proficient in DNA binding. Furthermore, biochemical complementation revealed that pi200 (copy-up) is dominant over wt pi35.0. The elevated activity of copy-up pi is not caused by an increased rate of replisome assembly as inferred from in vitro replication assays in which the lag periods observed were similar to that of wt pi35.0. Moreover, only one round of semiconservative, unidirectional replication occurred in all the samples analyzed indicating that copy-up pi proteins do not initiate multiple rounds of DNA synthesis. Rather, a larger fraction of DNA template replicates in the presence of copy-up pi as determined by electron microscopy. Two clusters of discrete DNA synthesis start sites are mapped by primer extension near the stability (stb) locus of the gamma ori. We show that the start sites are the same in the presence of wt pi35.0 or copy-up proteins. This comparative analysis suggests that wt pi35.0 and copy-up variants utilize fundamentally similar mechanism(s) of replication priming.

Amino Acid Substitution↗
PubMed1999

Genetic methods for characterizing the cis-acting components of yeast DNA replication origins.

Small circular plasmids containing replication origins and, in some cases, centromeres, can replicate autonomously in the nuclei of all tested yeast species. Because this autonomous replication is dependent on the replication origin within the plasmid, measurements of the efficiency of autonomous replication (by the methods summarized here) permit evaluation of the effects of mutations on origin function. Although alternative methods are available for genetic characterization of replication origins in other organisms, the simplicity of the autonomous replication assay in yeasts has permitted development of the deepest understanding to date of eukaryotic replication origin structure. This information has come primarily from studies with Saccharomyces cerevisiae. However, there are many other yeast species, each with its own variety of replication origins. Use of the methods summarized here to characterize origins in other yeast species is likely to provide additional insights into eukaryotic replication origin structure.

Cell Division↗
PubMed1993

Binding of bovine papillomavirus E1 to the origin is not sufficient for DNA replication.

Replication of the bovine papillomavirus (BPV-1) DNA requires both the viral E1 and E2 gene products. The minimal origin of replication, which resides in a 60-basepair fragment centered on the unique HpaI site of the BPV-1 genome, can be bound by the E1 protein and is flanked by E2 binding sites. The integrity of the region surrounding the unique HpaI restriction enzyme site is important for E1 binding and DNA replication, but the E2 binding sites are not required. The ability of E1 to complex with E2 and the requirement for both factors in DNA replication have led to the hypothesis that the E1/E2 complex may have a direct role in replication. Therefore we have studied mutations in the BPV-1 origin region for E1, E2, and E1/E2 complex binding and for their effect on transformation and replication in the context of the complete viral genome. Transformation and DNA replication were observed with some mutated viral genomes dramatically reduced for E1 binding. These mutated origins could bind significant amounts of E1 in the presence of E2, suggesting that binding of the E1/E2 complex could compensate for the loss of E1 binding in DNA replication. One mutation, with an eight-nucleotide insertion at the HpaI site, was still bound by E1 and the E1/E2 complex, yet did not replicate or transform efficiently. Thus although the binding of E1 or the E1/E2 complex to the origin appears to be necessary for replication, it is not sufficient.

Amino Acid Sequence↗
PubMed1985

Origin and initiation sites of lambda dv DNA replication in vitro.

The sequence of lambda DNA essential for the unique initiation of replication was analyzed in an in vitro replication system. Fragments of lambda DNA were inserted into pBR322 and used as templates or were circularized in vitro in the absence of pBR322 and employed in the same tests. A 165-bp region left of the EcoRI site in the O gene of the lambda genome was defined as the functional origin. This region, which we defined as the ori region, carries, in order, the 4 19-bp repeat sequences where the O protein binds (ori-repeats), an A+T-rich stretch, and a region that constitutes part of a large palindromic structure. Regions that have long been suspected to participate in lambda DNA replication initiation, ice and oop were not required for the O, P-dependent lambda-specific replication initiation. The lambda dv and the "ori region plus" recombinant plasmids initiated DNA synthesis at or around this region, and the reaction depended on the presence of lambda-coded initiators, O and P proteins. Early replicative intermediates of lambda dv were prepared in an in vitro replication system in the presence of ddCTP, an inhibitor of DNA chain elongation. This system allows only that DNA synthesis that is a result of replication initiation. Using this system, the initiation site(s) of the DNA synthesis was finely analyzed by mapping the transition sites from primer RNA to DNA synthesis. Short-chain DNAs produced from regions near the ori region were purified from the intermediates. A fraction of the short-chain DNAs was covalently linked to primer RNA. The 5'-ends that had been linked to RNA (transition sites) were exposed by alkaline hydrolysis, labeled with 32P, and the transition sites were mapped along the nucleotide sequence of the genome. Two striking features emerged from this analysis: (i) The transition sites are located on both sides of the ori region, and no transition arose within the 165-bp ori region; (ii) The transition sites on both sides are not unique, but multiple, and are clustered in one of the 2 strands. Furthermore, their orientation demonstrates that the DNA synthesis in initiation of replication from the 2 sides of the ori region converge. The frequency of the "leftward" DNA synthesis is several times higher than that of "rightward" synthesis. These results reflect asymmetric bidirectional replication of lambda dv DNA, and may also reflect replication of lambda phage DNA.

Bacteriophage lambda↗
PubMed1984

Replication of adeno-associated virus DNA. Complementation of naturally occurring rep- mutants by a wild-type genome or an ori- mutant and correction of terminal palindrome deletions.

When the entire adeno-associated virus (AAV) genome is inserted into a bacterial plasmid, infectious AAV genomes can be rescued and replicated when the recombinant AAV-plasmid DNA is transfected into human 293 cells together with helper adenovirus particles. We have taken advantage of this experimental system to analyze the effects of several classes of mutations on replication of AAV DNA. We obtained AAV mutants by molecular cloning in bacterial plasmids of naturally occurring AAV variant or defective-interfering genomes. Each of these mutants contains a single internal deletion of AAV coding sequences. Also, some of these mutant-AAV plasmids have additional deletions of one or both AAV terminal palindromes introduced during constructions in vitro. We show here that AAV mutants containing internal deletions were defective for replicative form DNA replication (rep-) but could be complemented by intact wild-type AAV. This indicates that an AAV replication function, Rep, is required for normal AAV replication. Mutants in which both terminal palindromes were deleted (ori-) were also replication defective but were not complementable by wild-type AAV. The cis-dominance of the ori- mutation shows that the replication origin is comprised in part of the terminal palindrome. Deletion of only one terminal palindrome was phenotypically wild-type and allowed rescue and replication of AAV genomes in which the deleted region was regenerated apparently by an intramolecular correction mechanism. One model for this correction mechanism is proposed. An AAV ori- mutant also complemented replication of AAV rep- mutants as efficiently as did wild-type AAV. These studies also revealed an unexpected additional property of the deletion mutants in that monomeric single-stranded single-stranded DNA accumulated very inefficiently even though monomeric single-stranded DNA from the complementing wild-type AAV did accumulate.

Autoradiography↗
PubMed1980

Preferred DNA sites are involved in the arrest and initiation of DNA synthesis during replication of SV40 DNA.

Previous analysis of simian virus 40 (SV40) DNA replication revealed a 2-4 fold excess of DNA molecules that were 90 +/- 2% replicated, demonstrating that replication forks accumulate near the termination site. To determine whether replication is arrested at specific DNA sites, forks were located on the SV40 genome by specifically 32P labelling 3' ends of nascent DNA on purified replicating SV40 DNA, isolating the longest 32P-DNA chains, annealing them to SV40 DNA and then digesting them with a restriction endonuclease that cut near the terminatin site. 32P-DNA fragments of several discrete lengths were released, demonstrating that replication forks on native chromosomes were arrested at preferred sites on the DNA. Most forks were arrested when bidirectional DNA replication was 91% completed, and the two forks were separated by about 470 bp of unreplicated DNA centered at the expected termination site. Forks were also arrested at other locations such that the center of the termination region defined by DNA arrest sites varied by +/- 450 bp. Electron microscopic analysis of replicating DNA suggested that such variation may result from asynchronous arrival of some replication forks. Analysis of 5' end-labeled nascent DNA demonstrated that initiation of Okazaki fragments was also promoted at preferred DNA sites (about 100-120 per genome). Thus specific DNA sequences appear to be utilized throughout DNA replication, not just at the origin.

Base Sequence↗
PubMed1995

Ultraviolet irradiation and c-jun over-expression regulates replication of polyoma sequences in WOP cells through a PEBP2 binding site.

Mouse fibroblast cells (WOP) express permissive factors which support polyoma DNA replication. However, electroporation into WOP cells of a mammalian expression vector that encodes the c-jun cDNA results in repression of polyoma DNA replication in a dose-dependent manner. In previous studies we have shown that UV-irradiation is capable of mediating a similar effect on polyoma DNA replication. When c-jun over-expression was combined with ultraviolet (UV)-irradiation, polyoma DNA replication decreased further. The repression of replication mediated by c-jun appears to be mediated by factor(s) that bind to PEBP4/2 target sequences as oligomers bearing the PEBP2/4 target site were capable of restoring polyoma DNA replication when added to UV-treated or c-jun over-expressing cells. The binding to the PEBP2/4 is partially dependent on the availability of AP-1 proteins, since an AP-1 target sequence can efficiently compete one of the three complexes formed with the PEBP2 target site. PEPB2 sequences do not, however, affect binding to the AP1 site. The effect of PEBP2 on polyoma replication is not dependent on the adjacent AP-1 site since PEBP2 could restore replication of polyomavirus which is mutated at the AP-1 sequence. A similar replication pattern was noted in a deletion mutant of polyoma which lacks PEBP4, yet, contains an intact PEBP2 binding sequence, suggesting that PEBP2 is the principle target for mediating repression of polyoma DNA replication.

Animals↗
PubMed1990

Analysis by in situ hybridization and autoradiography of sites of replication and storage of single- and double-stranded adenovirus type 5 DNA in lytically infected HeLa cells.

The distribution in the different compartments of infected nuclei of double-stranded (ds) and single-stranded (ss) adenovirus type 5 (Ad5) DNA and of the sites of viral DNA replication were examined on thin sections of Low-icryl-embedded material. The DNA is visualized with a biotinylated viral probe and immunogold labeling of biotin, and its replication is monitored by high-resolution autoradiography after short pulses with tritiated thymidine. The first detectable sites of viral DNA, named early replicative sites, contained all the ss and ds viral DNA and viral replicative activity. At a later stage of nuclear transformation, they gave rise to two new structures. The compact fibrillar ssDNA accumulation sites enlarged greatly and became transformed functionally to become a transient site of accumulation of large numbers of ss replicative intermediates. Double-stranded viral DNA and its replicative activity shifted primarily into immediately surrounding fibrillogranular peripheral replicative zones. Ad5 DNA replication continues in the ssDNA accumulation sites but it is intermittent, whereas in the peripheral replicative zones it is continuous. Still later in infection, a single, large, centrally located mass of dense fibrils, the viral genome storage site, developed in each nucleus which proved to be the main site of storage of nonreplicating, nonencapsidated, ds viral genomes. We discuss the possible distribution of the various viral DNA replicative intermediates among these virus-induced intranuclear structures.

Adenoviruses, Human↗
PubMed1995

A high capacity assay for inhibitors of human papillomavirus DNA replication.

The discovery of antiviral compounds against human papillomaviruses (HPV) has been hindered by the difficulties in culturing virus in vitro or assaying stable HPV DNA replication. However, plasmids containing the HPV replication origin replicate transiently upon co-transfection with HPV E1 and E2 expression vectors. We have adapted this assay using secreted alkaline phosphatase (SAP) as a reporter for rapid analysis of DNA copy number. Use of the SV40 early promoter in controlling SAP expression was critical in ensuring both a strong signal and copy number dependence: the stronger beta-actin promotor inhibited replication, while the weaker SV40 late promoter yielded very low levels of SAP. The precise configuration of the E1 and E2 expression vectors also was critical, most pre-existing vectors did not support efficient replication and SAP secretion. The extent of DNA replication and SAP secretion were both proportional to the amount of E1/E2 vector used in transfections; under optimal conditions SAP increased 100-fold during replication. The assay has been developed for compound screening in 96-well plates and several inhibitors have been identified. Quantitative Southern blot analysis has shown that most of these inhibit HPV DNA replication rather than SAP accumulation or activity, and several are under test in models of viral replication. The assay also provides a rapid system for functional analysis of the HPV E1, E2 genes and the replication origin.

Alkaline Phosphatase↗
PubMed2005

Impairment of replication fork progression mediates RNA polII transcription-associated recombination.

Homologous recombination safeguards genome integrity, but it can also cause genome instability of important consequences for cell proliferation and organism development. Transcription induces recombination, as shown in prokaryotes and eukaryotes for both spontaneous and developmentally regulated events such as those responsible for immunoglobulin class switching. Deciphering the molecular basis of transcription-associated recombination (TAR) is important in understanding genome instability. Using novel plasmid-borne recombination constructs in Saccharomyces cerevisiae, we show that RNA polymerase II (RNAPII) transcription induces recombination by impairing replication fork progression. RNAPII transcription concomitant to head-on oncoming replication causes a replication fork pause (RFP) that is linked to a significant increase in recombination. However, transcription that is codirectional with replication has little effect on replication fork progression and recombination. Transcription occurring in the absence of replication does not affect either recombination or replication fork progression. The Rrm3 helicase, which is required for replication fork progression through nucleoprotein complexes, facilitates replication through the transcription-dependent RFP site and reduces recombination. Therefore, our work provides evidence that one mechanism responsible for TAR is RNAP-mediated replication impairment.

DNA Helicases↗