Determination of DNA replication kinetics in synchronized human cells using a PCR-based assay.

Studies on the temporal order of DNA replication are difficult due to the lack of sensitivity of methods available for replication kinetic analysis. To overcome problems associated with the current techniques, we propose a PCR-based assay to determine the replication time of any single-copy DNA sequence in complex genomes. Human cells labeled with 5-bromodeoxyuridine (BrdU) were flow sorted, according to their DNA content, at different times after synchronous release from the G1/S phase boundary. The selective removal of newly-replicated BrdU-substituted DNA was achieved by UV light irradiation followed by S1 nuclease treatment. The timing of replication of selected DNA sequences (housekeeping, tissue-specific, and non-coding loci) was determined by polymerase chain reaction (PCR) amplification using appropriate primers. DNA sequences localized in inactive replication units allowed amplification whereas those that have replicated will not be amplified by PCR. Using this sensitive and quantitative assay the replication kinetic analysis of a number of different DNA sequences can be performed from a single sorting experiment.     

Density gradient analysis of newly replicated DNA from synchronized mouse lymphoma cells

The replication of DNA in synchronous cultures of mouse lymphoma cells was investigated by use of CsCl density gradient centrifugation. We found that the buoyant density of newly replicated DNA depended upon the particular stage of S phase in which synthesis occurred. In early S phase, newly replicated DNA exhibited buoyant densities which were slightly higher, on the average, than that of pre-existing DNA. As S phase progressed, newly replicated DNA shifted to lower buoyant densities, until, near the end of S phase, densities less than pre-existing DNA were observed. These observations are discussed in terms of their possible relevance to base compositional differences between nucleotide sequences made in early as opposed to middle or late S phase.     

Replication of yeast DNA and novel chromosome formation in mouse cells.

To determine whether yeast DNA can replicate or segregate in mammalian cells, we have transferred genomic DNA from the yeast Saccharomyces cerevisiae into mouse cells. Most of the lines contained stably integrated yeast DNA. However, in two of the lines, the yeast DNA was maintained as numerous small extrachromosomal elements which were still present after 26 cell divisions in selection but which were lost rapidly out of selection. This indicates that, although yeast DNA can replicate in mouse cells, the yeast centromere does not function to give segregation. In one cell line we observed a large novel chromosome consisting almost entirely of yeast DNA. This chromosome segregates well and contains mouse centromeric minor satellite DNA and variable amounts of major satellite DNA which probably comprise the functional centromere. The yeast DNA in the novel chromosome has a compacted chromatin structure which may be responsible for the efficient formation of anaphase bridges. Furthermore, yeast DNA integrated into mouse chromosomes forms constrictions at the point of integration. These features have previously been presumed to be hallmarks of centromeric function in transfection assays aimed at identifying putative centromeric DNA. Hence our results suggest caution be exercised in the interpretation of such assays.     

DNA synthesis in partially synchronized L cells

The synchronizing effects of lack of feeding and of 5-fluorodeoxyuridine on L cells in suspension culture were evaluated by serial estimations of the rate of incorporation of thymidine-2-¹⁴C into DNA. After 5 days without feeding, most of the cells remained viable and were partially synchronized. Temporary blockage of DNA synthesis with 5-fluorodeoxyuridine produced synchrony that was marked initially and then comparable to that following lack of feeding. In L cells under these conditions DNA synthesis occurred as a single wave ending just before division, in contrast to HeLa cells.     

Proliferation kinetics of endothelial and tumour cells in three mouse mammary carcinomas

Abstract. An autoradiographic study of three corded mouse tumours is reported. The proliferation characteristics of both tumour cells and endothelial cells were studied. The doubling time of these three tumours differed by a factor of 2.6 but there was only a small difference in the intermitotic time. All three tumours showed a very high cell loss factor (˜0.80) and the differences in growth rate resulted mainly from differences in the growth fraction .
The endothelial cell proliferation rates differed markedly in the three tumours, with labelling indices ranging from 18% in the faster tumours to 4.5% in the slowest. The potential doubling times for endothelium, calculated from these values, were much slower than the tumour cell cycle time or the tumour potential doubling time, but were two to four times faster than the volume doubling time of the tumour.
It appears likely that the endothelial proliferation rate influences the growth fraction, but similar high cell loss factors can occur in tumours with a four-fold difference in endothelial cell production rates. Inadequate branching of blood vessels seems likely to be at least as important as inadequate production of endothelial cells. It is not possible to determine whether slow tumour cell production evokes a slower endothelial growth or vice versa.     

Repetitive DNA sequence families in Crepis capillaris

Three families of tandemly repetitive DNA from Crepis capillaris were cloned and characterized. Data obtained from in situ hybridization indicate that these families are located mainly in the heterochromatic C-bands. The pCcH32 family hybridizes at the paracentromeric C-band of the NOR (nucleolus-organized region) chromosome and along most of the long arm of the same chromosome. The pCcD29 family is located in all the remaining C-bands of the karyotype, while the third family, pCcE9, is restricted to the more proximal C-bands. Nucleotide sequence comparisons between one cloned repeating unit from each DNA family showed some significant regions of homology between the families. We discuss the sequence relationships between the three DNA families and the significance of our data in relation to models of heterochromatin evolution, emphasizing the concepts of equilocality and the differentiation of the NOR-bearing chromosome. We also examine the possible role that chromosome disposition, in either mitotic or meiotic nuclei, plays in the distribution and homogenization of heterochromatic DNA sequences.     

Replication of mouse cytomegalovirus in thymidine kinase-deficient mouse cells.

In an attempt to determine whether mouse cytomegalovirus (MCMV) requires thymidine kinase (TK) for replication and whether it induces TK, TK-deficient mouse cells were isolated and used as host cells for MCMV. Mutant cells resistant to 200 μg/ml of 5-Bromodeoxyuridine (BUdR) were selected from SV40-transformed mouse cells, mks-A TU-7, by propagating the cells in the presence of varying concentrations of BUdR graded by serial 2-fold increments. The mutant cells, designated as TU-7 BU, showed a very low TK activity (less than 1/20 that of mks-A TU-7). Herpes simplex virus type 1 (HSV-1) replicated in starved as well as in unstarved TU-7 BU, whereas MCMV could replicate only in growing TU-7 BU and could not form plaques in monolayers of mks-A TU-7 or TU-7 BU. HSV-1 infection enhanced TK activity equally in both mks-A TU-7 and TU-7 BU. In contrast, TK activity of MCMV-infected mks-A TU-7 was lower than that of uninfected cells or cells inoculated with UV-inactivated virus. In addition, TK activity of the MCMV-infected TU-7 BU remained minimal without showing any increase. The replication of HSV-1 was completely inhibited in the presence of BUdR (10 μg/ml), whereas MCMV could replicate even in the presence of 50 μg/ml of BUdR. The results indicate that MCMV neither requires TK nor induces TK activity in the infected cells.     

Replication of repeated DNA in human cells

The replication pattern of the repeated sequence families of human DNA has been studied by means of DNA reassociation curves. Early- and late-replicating DNA fractions were obtained from synchronized cultures of KB cells by labeling cells with bromodeoxyuridine (BUdR) early or late in the DNA synthesis period and isolating the BUdR-containing DNA by CsCl density-gradient centrifugation. Highly repeated and moderately repeated sequence classes labeled with ${}^{14}\text{C-deoxycytidine}$ either early or late in the DNA synthesis period were also prepared. The effect of the isolated early- or late-replicating BUdR-DNA on the rate of reassociation of the ${}^{14}\text{C-labeled}$ repeated sequences was then tested. Increasing concentrations of early- or late-replicating BUdR-DNA were added to a constant amount of either ${}^{14}\text{C-labeled}$ early- or late-replicating repeated sequences, and the fraction of label in double-stranded DNA was determined. Analysis of the DNA reassociation curves so obtained indicates that some repeated sequence families are replicated throughout the DNA synthesis period whereas others are replicated primarily in the second half. This is true for both the highly-repeated and moderately-repeated sequence classes.     

Replication of polyoma plasmid recombinants in mouse cells

A series of pBR322 recombinants containing the intact early region and origin of replication of polyoma were constructed and tested for their ability to replicate in permissive mouse cells. During the first 60 hours after transfection of these plasmids into mouse cells there was an accumulation of material similar to that observed with non-cloned polyoma DNA, though none of the plasmids replicated up to as high a copy number as non-cloned polyoma DNA. The mouse-replicated plasmid DNAs had undergone changes in their methylation patterns consistent with their having been propagated in eukaryotic cells. They could be recovered efficiently by transfection back into Escherichia coli, and the structure of the recovered plasmids indicated that at least small plasmids were faithfully replicated in mouse cells.     

Clinical evaluation and mitochondrial DNA sequence analysis in three Chinese families with Leber's hereditary optic neuropathy

We report here the clinical, genetic, and molecular characterization of three Chinese families (WZ4, WZ5, and WZ6) with Leber's hereditary optic neuropathy (LHON). Clinical and genetic evaluations revealed the variable severity and age-of-onset in visual impairment in these families. Penetrances of visual impairment in these Chinese families were 33.3%, 35.7%, and 35.5%, respectively, with an average 34.8%. Furthermore, the average age-at-onset in those Chinese families was 17, 20, and 18 years. In addition, the ratios between affected male and female matrilineal relatives in these Chinese families were 3:0, 1:1, and 1.2:1, respectively. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical G11778A mutation associated with LHON in many families. The fact that mtDNA of those pedigrees belonged to different haplogroups F1, D4, and M10 suggested that the G11778A mutation occurred sporadically and multiplied through evolution of the mtDNA in China. However, there was the absence of functionally significant mutations in tRNA and rRNAs or secondary LHON mutations in these Chinese families. The I187T mutation in the ND1, the S99A mutation in the A6, the V254I in CO3, and I58V in ND6 mutation, showing high evolutional conservation, may contribute to the phenotypic expression of the G11778A mutation in the WZ6 pedigree. By contrast, none of mtDNA variants are evolutionarily conserved and implicated to have significantly functional consequence in WZ4 and WZ5 pedigrees. Apparently, these variants do not have a potential modifying role in the development of visual impairment associated with G11778A mutation in those two families. Thus, nuclear modifier gene(s) or environmental factor(s) seem to account for the penetrance and expressivity of LHON in these three Chinese families carrying the G11778A mutation.     

Synthesis and secretion of IgG in synchronized mouse myeloma cells

A mutant of the MPC-11 mouse myeloma cell line which grows as a monolayer has been used to study the synthesis and secretion of IgG in relation to the cell cycle. The mitotic detachment method has been used to obtain a pure population of mitotic cells which were then allowed to progress through the G1, S, and G2 phases of the cell cycle. The synthesis and the rate of secretion of IgG have been studied in each phase of the cycle by incubation of cells with ¹⁴C-amino acids, followed by immunoprecipitation and quantitation of synthesized and secreted IgG_2b. The data are consistent with the idea that synthesis and secretion of Ig are not a cell cycle dependent event in myeloma cells.     

Replication of mouse salivary gland virus in secondary mouse embryo cells

The replication of mouse salivary gland virus in mouse embryo cells was characterized by initiation of cell-associated virus accumulation at 16 to 20 hours post infection and free virus accumulation 20 to 24 hours post infection. Furthermore, the onset of cytopathic effects at 20 hours post infection coincided with development of infectious virus. MSGV synthesis was inhibited in the presence of FUdR under conditions where replication of VSV, an RNA virus, was unaffected.     

Effects of ultraviolet irradiation on the rate and sequence of DNA replication in synchronized Chinese hamster cells.

The effects of ultraviolet light (UV) irradiation on the rate of DNA replication in synchronized Chinese hamster ovary (CHO) cells were investigated. A technique for measuring semiconservative DNA replication was employed that involved growing the cells in medium containing 5-bromodeoxyuridine and subsequently determining the amount of DNA that acquired hybrid buoyant density in CsCl density gradients. One of the advantages of this technique was that it allowed a characterization of the extent of DNA replication as well as rate after irradiation. It was found that while there was a dose-dependent reduction in the rate of DNA replication following UV-irradiation, doses of up to 10 J/m2 (which produce many dimers per replication) did not prevent the ultimate replication of the entire genome. Hence, we conclude that dimers cannot be absolute blocks to DNA replication. In order to account for the total genome replication observed, a mechanism must exist that allows genome replication between dimers. The degree of reduction in the rate of replication by UV was the same whether the cells were irradiated at the G1-S boundary or 1 h into S-phase. Previous work had shown that cells in early S-phase are considerably more sensitive to UV than cells at the G1-S boundary. Experiments specifically designed to test for reiterative replication showed that UV does not induce a second round of DNA replication within the same S-phase.     

Replication termini in the rDNA of synchronized pea root cells (Pisum sativum)

In synchronized root cells of Pisum sativum (cv. Alaska) the joining of nascent replicons is delayed until cells reach the S-G(2) boundary or early G(2) phase. To determine if the delayed ligation of nascent chains occurs at specific termination sites, we mapped the location of arrested forks in the ribosomal DNA (rDNA) repeats from cells in late S and G(2) phases. Two-dimensional (neutral-alkaline) agarose electrophoresis and Southern blot hybridization with specific rDNA sequences show that only cells located at the S-G(2) boundary and early G(2) phase produce alkali-released rDNA fragments of discrete size. The released fragments are from a particular restriction fragment, demonstrating that the replication forks stop non-randomly within the rDNA repeats. Indirect end-labeling with probes homologous to one or the other end of the fork-containing restriction fragment shows that there are two termination regions, T(1) and T(2), where forks stop. T(1) is located in the non-transcribed spacer and T(2) is at the junction between the non-transcribed spacer and the 18S gene. The two termini are separated by 1.3 kb. Replication forks stop at identical sites in both the 8.6- and 9.0-kb rDNA repeat size classes indicating that these sites are sequence determined.