Role of RNA synthesis in DNA replication of synchronized populations of cultured mammalian cells

Using the harvesting method of synchronizing L cells, the relationship of RNA synthesis of DNA replication was studied by the use of selective inhibitors of RNA synthesis such as actinomycin D and chromomycin succinate. The synthesis of the early replicating DNA fraction is a process sensitive to the inhibition of RNA synthesis during the G1 period. The synthesis of early replicating DNA was inhibited by chromomycin succinate without affecting the initation of DNA synthesis. However, actinomycin D inhibited the synthesis of early replicating DNA and prevented the initiation of DNA synthesis in 50% of the synchronized cells. However, it was found that the continued synthesis of RNA during the S period is not essential for the synthesis of late replicating DNA. In addition to this specific response of DNA synthesis to the inhibitors of RNA synthesis, another function of early and late replicating DNA was determined relative to the cell viability. Cells synthesizing early replicating DNA were killed more efficiently by chromomycin than at other stages of the cell cycle. This indicates that the early replicating DNA unit plays a more important role in cell reproduction than the late replicating DNA unit.     

Topoisomerase II activity in the replicating DNA of irradiated hamster cells.

The activity of DNA topoisomerase II in the replicating DNA of irradiated Chinese hamster ovary cells was estimated by determining protein-linked DNA double-strand breaks generated in the presence of the DNA intercalative drug 4'-(9-acridinylamino) methanesulfon-m-anisidide. In the presence of this drug, DNA double-strand breaks were produced at the same rate, and with the same overall frequency, in both the bulk and the newly synthesized DNA of control cells and cells irradiated with 10 Gy. The results indicate that DNA topoisomerase II is fully active in the replicating DNA of irradiated cells and is distributed at a frequency similar to that in parental DNA.     

Effect of damage to early, middle, and late-replicating DNA on progress through the S period in Chinese hamster ovary cells

In order to explain sequential replication of DNA in eukaryotic cells, the duplication of a given bank of replicons is proposed to be initiated by specific events coupled to synthesis of the preceding replicons in the sequence. This model predicts that DNA synthesis in mid or late S should depend upon the synthesis and/or integrity of previously replicating DNA, but should not depend upon the integrity of DNA replicating later in the sequence. By incorporating BUdR into DNA during a given short interval of one S period in synchronous Chinese hamster ovary cells, we are able to selectively damage this DNA by irradiation at selected times before or during the next S period. Utilizing this technique, we find that damage to early replicating DNA before entry into the second S phase markedly suppresses DNA synthesis in the entire S period. Damage to mid or late replicating DNA prior to entry into the second S period has no effect on early S, but markedly reduces DNA synthesis commencing in mid or late S, respectively. Furthermore, if early replicating DNA is damaged with light in mid-S, no effect on subsequent DNA synthesis is observed. These results can be fitted to a model in which sequential triggering of replicon synthesis promotes orderly progression through S.     

Establishment of infection by spleen necrosis virus: inhibition in stationary cells and the role of secondary infection

The relationship of two early events in the establishment of infection by avian retroviruses, the inhibition of viral DNA synthesis in stationary avian cells and the secondary infection which occurs after infection of replicating cells, was investigated. When neutralizing antibody to spleen necrosis virus was used to prevent secondary infection, the amount of unintegrated linear spleen necrosis virus DNA detected was much lower in infected stationary cells than in infected replicating cells. The amount of unintegrated linear spleen necrosis virus DNA in stationary cells was less than one copy per cell even at high multiplicities of infection. Viral DNA synthesis resumed after stimulation of the cells to replicate. The time of this viral DNA synthesis was closely correlated with renewed cellular DNA synthesis. In addition, blocking secondary infection of replicating cells prevented the rate of virus production from reaching the high levels usually associated with a normal productive infection by SNV. Virus production increased if secondary infection was allowed. However, this rise in virus production was not proportional to the amounts of viral DNA integrated after secondary infection.     

Bacterial nucleic acid synthesis in plants following bacterial contact

Summary After plants have been in contact with a suspension of bacteria one finds in plant cells self replicating bacterial DNA and replicating molecules formed of bacterial DNA combined with plant DNA. Moreover newly synthesized bacterial RNA appears in the host cell. These phenomena seem to be due to a transfer of bacterial DNA into plant cells.     

DNA synthesis in polyoma virus infection. III. Mechanism of inhibition of viral DNA replication by cycloheximide.

The formation of viral DNA was inhibited in polyoma virus-infected cells in which protein synthesis had been blocked by cycloheximide. The present studies show the following. (i) The pool of replicating viral DNA molecules was reduced in cycloheximide-treated cells by an amount consistent with inhibition of [3-H]thymidine incorporation into viral DNA, whereas the rate of turnover of the replicating population was not affected. (ii) The rate of conversion of replicating molecules into closed-circular DNA was not affected by cycloheximide. (iii) The rate of elongation of nascent viral DNA fragments into strands of unit genome length was unaffected by cycloheximide. It is concluded that viral DNA synthesis is inhibited in the absence of protein synthesis exclusively at the level of initiation of new rounds of genome replication. Replicating molecules already initiated at the time of addition of cycloheximide matured into progeny closed-circular DNA at a normal rate.     

Proteasome inhibitors alter the orderly progression of DNA synthesis during S-phase in HeLa cells and lead to rereplication of DNA

Replication of the mammalian genome occurs only once per cell cycle and is under strict spatiotemporal control. DNA synthesis first takes place in the inner nucleus and moves gradually to the area subjacent to the nuclear membrane as S-phase progresses. We found that proteasome inhibitors specifically reduce DNA synthesis from later replicating origins but not that from earlier replicating origins. When MG132 was added in mid S-phase and washed off in late S-phase, however, DNA synthesis resumed not at the nuclear periphery, where it was last seen, but back in the inner nucleus. Analysis of DNA from these cells showed that mid to late replicating genes were rereplicated resulting in the overreplication of DNA. Our results suggest the existence of proteasome-dependent mechanisms regulating the orderly progression of S-phase. The transient treatment of mid S-phase cells with MG132 resulted in overreplication of DNA providing an easy experimental method to perturb the "once per cell cycle" control of genome replication in mammalian cells.     

Preferential modification of replicating DNA by benz(a)pyrene)

The nuclei of cells from regenerating rat liver were incubated with benzo(a)pyrene and the concentrations of the metabolites that covalently bound to DNA of different nuclear fractions were compared. It appeared that DNA associated with nuclear matrix (containing replicating DNA) is modified most intensively. The synchronized mouse embryo cells were incubated with benzo(a)pyrene during S phase and the levels of modifications in short and long single-stranded DNA fragments were compared. It has been observed that replicating DNA is represented in short fragments. These short DNA fragments were found to be modified by benzo(a)pyrene 4-9 times more intensively than total DNA. The possible mechanisms of both the increase in the number of DNA modifications in proliferating cells and the reason for the enhancement of carcinogenic effect on dividing cells are being discussed.     

Identification of late DNA-replicating regions in Chinese hamster chromosomes using a BrdU-giemsa technique

Asynchronous Chinese hamster cells were labelled with BrdU for 3 h prior to harvesting the metaphase cells. The late DNA replicating sites became unifilarly BrdU-substituted as compared to the earlier replicating sites having a normal DNA constitution. Those late replicating sites were identified by pale coloration or dot formation after treatment with 1.0 M Na-phosphate solution (adjusted to pH 9.0 with supersaturated amount of NaHCO₃ and at a temperature of 69–75° C) and staining with Giemsa dye. Using this technique, nuclei with incorporated BrdU could be distinguished from nuclei that had not incorporated BrdU. — One of the advantages of using this technique for identification of late DNA replicating sites is that cells are treated continuously with BrdU for a short period of time before harvesting and only one sampling, rather than a series of samplings, is required to achieve a clear-cut result.     

Mechanisms and age-specific characteristics of nuclear DNA replication

Replication mechanisms of nuclear DNA in eucaryotic cells and their changes with the organism aging are discussed. Tge polyrepliconic nature of replicating DNA, discontinuous synthesis of its newly formed chains, enzymic apparatus of replication and regulation of this process are described. Special attention is paid to destabilization of the secondary structure of the replicating molecule. In aging, changes in the DNA replication were found at each level of its regulation, i.e. at synthesis precursors, enzymic replication complex and replicating DNA structure. This may be an indication of the altered regulation of the DNA replication with aging.     

Sizes and rates of elongation of replicons in the frog embryo

Summary DNA fiber autoradiography has shown an increase in size of replicons during early development of the frog embryo. Replicons of endoderm cells were considerably larger than those of dorsal ectoderm and mesoderm cells in tailbud embryos. Late replicating DNA in partially synchronized tailbuds has a more rapid rate of replicon elongation than does early replicating DNA.     

Letter: Some unusual properties of replicating adenovirus type 2 DNA

Replicating adenovirus type 2 DNA was isolated from KB cells 13 hours after infection. The buoyant density in caesium chloride of the replicating DNA was found to be 5 to 10 mg/cm² greater than that of mature adenovirus type 2 DNA. The single-strand specific nuclease from Neurospora crassa released 25 to 30% of the radioactivity from replicating DNA and the density difference between replicating and mature adenovirus DNA was eliminated after digestion with this enzyme, but not after digestion with RNase or pronase. The results suggest that the complementary strands of adenovirus type 2 DNA are replicated asynchronously.     

Amplification of portions of the genome in mammalian somatic cells resistant to colchicine. VI. Restriction analysis of the amplified DNA sequences

Fragments specific for the amplified regions in DNA of Djungarian hamster colchicine-resistant cells were studied after restriction endonuclease digestion. We used three different methods of detection of these fragments: a) comparison of the wild type and resistant cell DNA electroforegramms stained by ethidium bromide; b) blotting of DNA from sensitive and resistant variants onto nitrocellulose filters and their hybridization with nick-translated DNA from resistant cells, in the presence of the excess of unlabelled DNA from the wild type cells (competitive hybridization); c) investigation of autonomously replicating DNA from sensitive and colchicine-resistant sublines. The highest resolution was found using the third method. However, the competitive hybridization is evidently a more universal approach to restriction analysis of DNA amplified sequences, because it gives quite high resolution and may be used for studying both autonomously and non-autonomously replicating sequences.     

Heterogeneity in the replicating population of cultured human epidermal keratinocytes

We studied the replication of keratinocytes in stratified squamous epithelia. Other studies have revealed functional and morphological heterogeneity in the replicating population of such cells. To examine possible kinetic heterogeneity, we determined the cell-cycle lengths of replicating cells in cultures of human epidermal keratinocytes. A double-label assay was developed, which measures the time between two successive cycles of DNA synthesis. The first cycle of DNA synthesis was marked by pulse labeling cultures for a brief period with 14C-thymidine (dThd), and the second cycle was detected by labeling at a later time with bromodeoxyuridine (BrdUrd). The time taken for the 14C-labeled DNA to become doubly labeled with BrdUrd was shown to correspond to the length of the cell cycle. In subconfluent cultures in which the cell number increased at an exponential rate, the average cell-cycle time was 21.5 h. In confluent cultures in which desquamation was balanced by cell renewal, the average cell cycle was 31.5 h. However, in confluent cultures, three populations of replicating cells were evident, these having cycle times of 22, 33, and 40 h. In subconfluent cultures, there was no clear evidence for cell-cycle heterogeneity of the replicating cells, although the most rapidly cycling cells in these cultures had a cycle time (16 h) considerably less than the most rapidly cycling cells in the confluent cultures (21 h). It is possible that the rapidly cycling cells seen in the subconfluent cultures were stem cells.(ABSTRACT TRUNCATED AT 250 WORDS)     

Possible role of H1 histone in replication timing

AT‐rich repetitive DNA sequences become late replicating during cell differentiation. Replication timing is not correlated with LINE density in human cells (Ryba et al. 2010). However, short and properly spaced runs of oligo dA or dT present in nuclear matrix attachment regions (MARs) of the genome are good candidates for elements of AT‐rich repetitive late replicating DNA. MAR attachment to the nuclear matrix is negatively regulated by chromatin binding of H1 histone, but this is counteracted by H1 phosphorylation, high mobility group proteins or, indirectly, core histone acetylation. Fewer MAR attachments correlates positively with longer average DNA loop size, longer replicons and an increase of late replicating DNA.     

Changes in nucleosome repeat lengths precede replication in the early replicating metallothionein II gene region of cells synchronized in early S phase

Previous investigations showed that inhibition of DNA synthesis by hydroxyurea, aphidicolin, or 5-fluorodeoxyuridine produced large changes in the composition and nucleosome repeat lengths of bulk chromatin. Here we report results of investigations to determine whether the changes in nucleosome repeat lengths might be localized in the initiated replicons, as postulated [D'Anna, J. A., & Prentice, D. A. (1983) Biochemistry 22, 5631-5640]. In most experiments, Chinese hamster (line CHO) cells were synchronized in G1, or they were synchronized in early S phase by allowing G1 cells to enter S phase in medium containing 1 mM hydroxyurea or 5 micrograms mL-1 aphidicolin, a procedure believed to produce an accumulation of initiated replicons that arise from normally early replicating DNA. Measurements of nucleosome repeat lengths of bulk chromatin, the early replicating unexpressed metallothionein II (MTII) gene region, and a later replicating repeated sequence indicate that the changes in repeat lengths occur preferentially in the early replicating MTII gene region as G1 cells enter and become synchronized in early S phase. During that time, the MTII gene region is not replicated nor is there any evidence for induction of MTII messenger RNA. Thus, the results are consistent with the hypothesis that changes in chromatin structure occur preferentially in the early replicating (presumably initiated) replicons at initiation or that changes in chromatin structure can precede replication during inhibition of DNA synthesis. The shortened repeat lengths that precede MTII replication are, potentially, reversible, because they become elongated when the synchronized early S-phase cells are released to resume cell cycle progression.     

The secondary structure and nitrocellulose affinity of freshly replicated DNA from Ehrlich ascites cells (author's transl)]

Hydroxyapatite chromatography and isopycnic Cs2SO4 centrifugation normally yield no indications of single-stranded DNA when that fraction of replicating DNA from Ehrlich ascites cells which can be separated by nitrocellulose chromatography is analyzed. Single-stranded DNA is detected by both methods if the DNA is fragmented by ultrasound before the nitrocellulose chromatography. The digestion of this DNA fraction by single-strand-specific nucliase leads to a loss of its binding to nitrocellulose and of the indications of single-stranded DNA. The loss for the affinity to nitrocellulose is also observed when the corresponding fraction separated from unfragmented DNA is digested by endonuclease. It is suggested that replicating DNA is bound to nitrocellulose by means of single-stranded gaps on the replication fork. These gaps are apparently too small to be detected within large, otherwise entirely double-stranded molecules by hydroxyapatite chromatography and Cs2SO4 centrifugation. In the case of nitrocellulose-binding ultrasound fragments, this relation seems to be more favorable because of the separation of most of the residual double-stranded part. It is demonstrated that sonication of helical DNA also generates a small amount of fragments with some single-stranded character. The effects observed with replicating DNA could be distinguished from these artifacts.     

Coiled Rings of DNA Released from Cells Infected with Bacteriophages T7 or T4 or from Uninfected Escherichia coli

The replicating intracellular DNA of phage T7 was labeled at high specific activity with tritiated thymidine. The DNA of uninfected Escherichia coli was similarly labeled. Portions of cells which contained replicating phage T7 or E. coli DNA were lysed by a lysozyme, freeze-thaw, sodium lauryl sulfate procedure, and the DNA was spread on Millipore membranes for visualization by autoradiography. The DNA of phage T7 appeared to be highly concatenated reaching lengths of up to 721 mum. Much of the DNA of phage T7 and E. coli was retained in compact globular structures. In addition, orderly coiled rings of varying diameter up to about 43 mum were regularly observed. Similar coiled ring structures were also observed in autoradiographs of replicating phage T4 DNA which had been prepared in previous experiments. Worcel and Burgi (27) have presented evidence that E. coli chromosomes, when gently extracted from cells, are in a multilooped and superhelically twisted configuration. The coiled rings which we have observed may correspond to the relaxed, multilooped configurations which they find when the superhelical twists have been relieved by one or more nicks in each loop.     

Chromosome replication and synthesis of non-histone proteins in giant polytene chromosomes

Synthesis of chromosomal proteins was studied by means of autoradiography in giant polytene chromosomes of Chironomus thummi. Incorporation of tryptophane-H₃ into non-histone proteins of the chromosome does not increase during DNA synthesis. Grain count data reveal that chromosomes of cells which are actively replicating DNA do not differ from non-replicating cells in regard to the incorporation of tryptophane-H₃ into chromosomal non-histone protein. Chromosomes of cells which are replicating DNA incorporate about 2 times more lysine-H₃ than do non-DNA replicating cells. Synthesis of histones accounts for this increase in lysinc-H₃ incorporation. This investigation was supported in part by U.S.P.H.S. fellowship number F2CA-23, 971-01A4 from the National Cancer Institute.