Replication of repeated DNA in human cells

Eukaryotic DNA replication

One of the fundamental characteristics of life is the ability of an entity to reproduce itself, which stems from the ability of the DNA molecule to replicate itself. The initiation step of DNA replication, where control over the timing and frequency of replication is exerted, is poorly understood in eukaryotes in general, and in mammalian cells in particular. The cis-acting DNA element defining the position and providing control over initiation is the replication origin. The activation of replication origins seems to be dependent on the presence of both a particular sequence and of structural determinants. In the past few years, the development of new methods for identification and mapping of origins of DNA replication has allowed some understanding of the fundamental elements that control the replication process. This review summarizes some of the major findings of this century, regarding the mechanism of DNA replication, emphasizing what is known about the replication of mammalian DNA. J. Cell. Biochem. Suppls. 32/33:1-14, 1999.

A model for the spatio-temporal organization of DNA replication in mammalian cells

The spatio-temporal organization of chromosomal DNA replication was analyzed using a model based on a "DNA unit" (or decondensation unit) hypothesis. The model is an extension of the fork movement theory of Huberman & Riggs (1968) and can account for a partially deterministic and partially stochastic order of DNA replication in chromosomes. It presumes that each chromosome is composed of DNA units that are arranged in sequence and that are replicated in parallel. A deterministic wave of chromatin decondensation propagates along the DNA unit continuously and progressively providing a field for the random activation of replication origin. Assignment of replication times to DNA compartments by a Monte Carlo method was programmed based on the model and the program was used to stimulate DNA synthesis rate curves that can be measured by the method of Dolbeare et al. (1983, 1985). The shape of the curve is shown to constrain possible parameter values of the model, which include the rate of fork movement, the fraction of chromatin that is decondensed at the start of S-phase, the initial number of origins activated, the rate at which new origins are activated, etc. The chromosomal organization that controls the molecular level of DNA replication is briefly reviewed and its relevance to the model is also discussed.

Replication of non-repetitive DNA during early, middle and late S phase. The general class and the subset transcribed

Synchronized cultures of Chinese hamster ovary cells were pulse-labelled with 5-bromodeoxyuridine (BrdU) during early (0-2.0 h), middle (2.5-4.0 h) and late (4.5-6.0 h) S phase in two successive cell cycles. In each case, the DNA containing BrdU in both strands was duplicated at the same time in both cycles and was isolated for further characterization by centrifugation in CsCl gradients. These DNAs were then radiolabelled by nick-translation and used in either DNA-DNA or RNA-DNA hybridization experiments. In the DNA-DNA experiments, advantage was taken of the substantial rate increases attainable in high concentrations of dextran sulfate to obtain complete reassociation curves with relatively small amounts of material. Assuming that no unresolved low repetition frequency components exist, renaturation kinetics suggest that early replicating DNA contains a greater proportion of non-repetitive sequences than DNA synthesized at later times, the order being early greater than middle greater than late. However, in terms of complexity the non-repeated DNA duplicated early had only 74% of the diverse sequences present in log-phase cells, whereas that replicated in middle and late S phase had 82 and 79.5%, respectively. It therefore appears that while DNA synthesized at different times in S phase may contain varying proportions of non-repetitive sequences, when their diversity is taken into account very few of these sequences (25% or less) exhibit temporal control of replication. Finally, measurements with total cell RNA indicated that the transcribed fraction of non-repeated DNA showed a slight preference for replication in early S phase.

Differential transcription of early and late-replicating DNA in human cells

Several studies suggest that most of the functional genes of mammalian cells are contained in the early-replicating sequences of DNA. There is little direct evidence, however, to support this view. To determine whether the extent of transcription of different DNA sequences is related to the order in which these sequences are replicated, I have selectively labelled early- and late-replicating DNA with [3H]thymidine ([3H[TdR) and determined the extent to which the 3H-labelled non-repeated sequences of each DNA preparation are hybridized by increasing concentrations of RNA from exponentially growing KB cells. The fraction of DNA hybridized at infinite RNA concentration was then estimated by a plotting method which linearizes the data. Selective labelling of DNA was achieved by synchronizing a culture of KB cells by a double block of DNA synthesis and then labelling portions of the culture 0-3 h (early) or 6-9 h (late) after release of the cells from the second block. At all RNA concentrations tested, the fraction of early-replicating DNA hybridized was significantly greater than that of late-replicating DNA. At infinite RNA concentration the value for early-replicating DNA was 3-4 times as great as that of late-replicating DNA. If it is assumed that the fraction of DNA hybridized at infinite RNA concentration is proportional to the fraction of DNA which is transcribed, it can be concluded that 3-4 times as much early-replicating DNA is transcribed as late-replicating DNA in exponentially growing KB cells.

Amplified dihydrofolate reductase genes are located in chromosome regions containing DNA that replicates during the first half of S-phase

To obtain a better understanding of the relationship between metaphase chromosome banding patterns and genome organization, attention was focused on regions of metaphase chromosomes that were found to contain the genes for a specific cellular enzyme, dihydrofolate reductase (DHFR). These studies involved the use of highly methotrexate-resistant mouse lymphoblastoid cells (L5178YR), which contain approximately 300 times the number of DHFR genes present in parental cells (L5178YS). Karyotypic analysis revealed the presence of two very large, nonhomologous, marker chromosomes that were absent in the parental line. In situ hybridization of 3H-labeled cloned DHFR cDNA to metaphase chromosomes of L5178YR cells was used to localize the DHFR genes to a very large Giemsa (G)-negative region on each of the two large marker chromosomes. Regional patterns of DNA replication in metaphase chromosomes were studied by autoradiographic visualization of [3H]thymidine incorporation and by fluorescent microscopic visualization of bromodeoxyuridine incorporation. Because the amplified DHFR genes were present within two prominent cytogenetic regions on two easily identifiable chromosomes, it was possible to observe the following. The amplified DHFR genes were located in chromosome regions that replicated at the same time during the first half of a 9-h-S-phase. DNA replication began simultaneously and terminated simultaneously at many locations throughout each amplified region. We conclude that transcriptionally active DHFR genes are located within large G-negative regions of metaphase chromosomes and that the DNA within these regions replicates during the first half of S-phase.

Ordered replication of DNA sequences: synthesis of mouse satellite and adjacent main band sequences

The replication of mouse satellite DNA was delayed when synchronized 3T3 cells were exposed to low concentrations of hydroxyurea during S phase, It appears that the onset of satellite replication is not a time dependent event, but instead requires that a certain amount of main band DNA be synthesized first. Using hydroxyapatite chromatography and S1 nuclease digestion, a procedure was developed to quantitate the synthesis of both satellite and neighboring main band sequences. The replication kinetics of satellite determined by this method agree with previous estimates. Main band sequences adjacent to satellite appear to replicate in concert with satellite DNA. The results are discussed and related to the limitations of the techniques utilized.