Intermittent DNA synthesis and periodic expression of enzyme activity in the cell cycle of WI-38

Quantifying DNA replication speeds in single cells by scEdU-seq

In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2'-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.

Evolution of the clock from yeast to man by period-doubling folds in the cellular oscillator

Analysis of genome-wide oscillations in transcription reveals that the cell is an oscillator and an attractor and that the maintenance of a stable phenotype requires that maximums in expression in clusters of transcripts must be poised at antipodal phases around the steady state-this is the dynamic architecture of phenotype. Plots of the path through concentration phase space taken by all of the transcripts of Saccharomyces cerevisiae yield a simple three-dimensional surface. How this surface might change as period lengthens or as a cell differentiates is at the center of current work. We have shown that changes in gene expression in response to mutation or perturbation by drugs occur through a folding or unfolding of the surface described by this circle of transcripts and we suggest that the path from this 40-minute oscillation to the cell cycle and circadian rhythms takes place through a series of period-two or period-three bifurcations. These foldings in the surface of the putative attractor result in an increasingly dense set of nested trajectories in the concentrations of message and protein. Evolutionary advantage might accrue to an organism that could change period by changes in just one or a few genes as day length increased from 4 hours in the prebiotic Earth, through 8 hours during the expansion of photoautotrophs, to the present 24 hours.

Chromosome organization and chromatin modification: influence on genome function and evolution

Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.

Eukaryotic DNA replication is a topographically ordered process

This paper describes the relationship between the BrdUrd replicating pattern of a cell and its localization within the S phase by means of topographical features and DNA content measurement. The present study follows an objective ranking of the BrdUrd patterns obtained from a spectral analysis of the BrdUrd images. The pattern ranking was consistent with the DNA content increase throughout the S phase. Five texture groups were arbitrarily set up for the purpose of multivariate analysis. Nine topographical parameters were computed for each BrdUrd-labelled nucleus. The descriptive quality of these parameters was assessed by means of factorial discriminant analysis. These parameters made it possible to characterize objectively the known pattern distributions of replication sites qualitatively described in the literature.

Subdivision of S-phase by analysis of nuclear 5-bromodeoxyuridine staining patterns

After pulse labeling of mammalian cells in vivo or in vitro with 5-bromodeoxyuridine (BrdUrd), followed by immunostaining with a monoclonal antibody to DNA-incorporated BrdUrd, various intranuclear staining patterns are observed. These results are obtained in various labeling, fixation, denaturation, and staining conditions. We defined five different patterns in immunoperoxidase-stained monolayers of human and rodent cancer cells and compared mean nuclear areas as measured by computerized planimetry. Furthermore, we evaluated frequency distributions of these patterns in partly synchronized cell populations and correlated these results with flow cytometric DNA histograms. The results indicate that the observed patterns reflect the spatial and temporal organization of DNA synthesis, which seems to be characterized by at least three successive stages of replication. Evaluation of these patterns may have various applications in studies on cell cycle kinetics.

Role of replication time in the control of tissue-specific gene expression

Late-replicating chromatin in vertebrates is repressed. Housekeeping (constitutively active) genes always replicate early and are in the early-replicating R-bands. Tissue-specific genes are usually in the late-replicating G-bands and therein almost always replicate late. Within the G-bands, however, a tissue-specific gene does replicate early in those cell types that express that particular gene. While the condition of late replication may simply be coincident with gene repression, we review evidence suggesting that late replication may actively determine repression. As mammals utilize a developmental program to Lyonize (facultatively heterochromatinize) whole X chromosomes to a late-replicating and somatically heritable repressed state, similarly another program seems to Lyonize individual replicons. In frogs, all genes begin embryogenesis by replicating during a very short interval. As the developmental potency of embryonic cells becomes restricted, late-replicating DNA gradually appears. This addition to the repertoire of gene control--i.e., repression via Lyonization of individual replicons--seems to have evolved in vertebrates with G-bands being a manifestation of the mechanism.

Flow cytometric estimation of cell cycle parameters using a monoclonal antibody to bromodeoxyuridine

An estimation of cell kinetic parameters was made by simultaneous flow cytometric measurements of DNA and bromodeoxyuridine (BrdUrd) contents of cells. The procedure described in this paper involves the incorporation of BrdUrd by S phase cells, labeling the BrdUrd with an indirect immunofluorescent technique using a monoclonal anti-BrdUrd antibody, and staining DNA with propidium iodide (PI). The amount of incorporated BrdUrd in HeLa cells was proportional to that of synthesized DNA through S phase. For all cell lines examined, the pattern of BrdUrd incorporation was essentially the same and the rate of DNA synthesis during S phase was not constant. The bivariate BrdUrd/DNA distributions showed a horse-shoe pattern, maximum in the mid S phase and minimum in the early and late S phases. Furthermore, the durations of cell cycle (Tc) and S phase (Ts) were estimated from a FLSm (fraction of labeled cells in mid S phase) curve that was generated by plotting the percentage of BrdUrd pulse-labeled cells in a narrow window defined in the mid S phase of the DNA histogram. The values of these parameters in NIH 3T3, HeLa S3, and HL-60 cells were in good accordance with the reported data. This FCM method using the monoclonal anti-BrdUrd antibody allows rapid determination of both cell cycle compartments and also Ts and Tc without the use of radioactive DNA precursors.

DNA synthesis rate changes during the S phase in mouse epidermis

The in vivo DNA synthesis rate throughout the S phase of mouse epidermal cells was investigated. Epidermal basal cells were isolated at various times of the day from normal animals injected with [3H]TdR 30 min before sacrifice, and from pulse-labelled animals with regenerating and growth-inhibited epidermis. The cells were analysed by DNA flow cytometry combined with cell sorting. Cells from successive fractions of the S phase were sorted on glass slides and subjected to quantitative [3H]TdR autoradiography. The results confirmed the presence of unlabelled (slowly replicating) cells in the S phase, the proportion of which was circadian stage-dependent with minimum values at midnight and in the early morning. The DNA synthesis rate throughout the S phase showed a general trend with high values in the mid-fractions, a pattern which was similar in normal and in growth perturbed epidermis. In the early morning the DNA synthesis rate pattern was bimodal with maxima both in the first and second half of the S phase, with a corresponding trough in mid-S. At this time of day the cell progression rate through S is at its maximum, indicating a relationship between the overall DNA synthesis rate and the rate distribution pattern through S.

Total LD and isozyme variations during in vitro fibroblast aging with a discussion of its theoretical implication

Dermal fibroblast cultures were obtained from 18 patients. Total lactic dehydrogenase (LD) and LD isozymes were determined after each population doubling (PD). The lactic dehydrogenase was assayed by the method of Wacker, Ulmer and Vallee. The isozymes were analyzed by gel electrophoresis. Some investigators have reported conflicting results as to the quantity of LD produced during in vitro aging. These researchers sampled a small number of PDs. We found that the total LD varied with each PD. A distinct isozyme pattern has been described for adult, fetal and neoplastic fibroblasts. We have found all three patterns occurring during the in vitro aging of our normal diploid fibroblasts. In spite of our asynchronous population of cells the LD and its isozymes continually fluctuate. An asynchronous population of cells would be expected to produce a dampening of the total LD. In order to explain this finding we speculate a synchrony is established in a "gated" entrance from subcycle Gq into the S stage or from G1 and G0 into the S stage. In order to evaluate, accurately, changes occurring during in vitro aging it is imperative to assay each PD.

Altered expression of ribokinase activity in Novikoff hepatoma variants

Ribokinase, the first enzyme in ribose catabolism, is altered in its expression in ribose-utilizing Novikoff hepatoma variants. 90% of the variants selected for their ability to use D-ribose as a sole carbon source show a change in ribokinase activity. After non-selective growth, phenotypically unstable variants lose their altered expression and regain a parental form of expression of this enzyme. In the variants, ribokinase expression in non-inducible by the carbon source and is unaffected by the growth phase of the cells. However, ribokinase expression in both parental cells and variants is cell cycle-dependent. Parental Novikoff hepatoma cells have three peaks of ribokinase activity during the S, G2 and M phases. Variants are described which have high basal levels of ribokinase and only a single peak of enzymatic activity during the S phase. In addition to changes in the level of ribokinase, changes in the subcellular localization of the enzyme have been found in some variants. While the change in the level of ribokinase seems to be a property of the variant isolated, the change in subcellular location of ribokinase can be readily achieved by culture conditions.

Rates of incorporation of radioactive molecules during the cell cycle

We report measurements of the incorporation of radioactive molecules during short labeling periods, as a function of cell-cycle stage, using a cell-sorter-based technique that does not require cell synchronization. We have determined: (1) tritiated thymidine (3H-TdR) incorporation throughout S-phase in Lewis lung tumor cells in vitro both before and after treatment with cytosine arabinoside; (2) 3H-TdR incorporation throughout S-phase in KHT tumor cells in vitro and in vivo; (3) 3H-TdR incorporation throughout S-phase in Chinese hamster ovary cells and compared it with DNA synthesis throughout S-phase; (4) a mathematical expression describing 3H-TdR incorporation throughout S-phase in Chinese hamster M3-1 cells; and (5) the simultaneous incorporation of 3H-TdR and 35S-methionine as they are related to cell size and DNA content in S49 mouse lymphoma cells. In asynchronously growing cells in vitro and in vivo, 3H-TdR incorporation was generally low in early and late S-phase and highest in mid-S-phase. However, in Lewis lung tumor cells treated with cytosine arabinoside 3H-TdR incorporation was highest in early and late S-phase and lowest in mid-S-phase. Incorporation of 35S-methionine increased continuously with cell size and DNA content. Incorporation of 3H-TdR in CHO cells was proportional to DNA synthesis.

Mapping the mitotic clock by phase perturbation

In synchronized V79 cells perturbed by serum, heat shock, or ionizing radiation at half-hour intervals through a modal 8.5-hour cell cycle, phase-response curves show a characteristic biphasic pattern of advances and delays in subsequent cell divisions. These observations, together with previous observations of quantizement of generation times in this an other cell lines have led us to consider a model incorporating, in the simplest case, a two-component oscillator with two threshold crossings required per cell cycle. By assuming that oscillator variables respond in a simple way to the experimental perturbations, for example, by first order destruction due to heat shock, a map of the qualitative features of the oscillator can be obtained by matching simulated with experimental phase response curves. Random fluctuations in oscillator variables about a fixed trajectory lead to subthreshold oscillations and result in a distribution of generation times which is roughly a negative exponential, but quantized within this exponential envelope. The extent of the random fluctuations can be determined from comparison with data on desynchronization of a cell population after mitotic selection. The same parameters which correctly simulate phase response and the desynchronization data also give good agreement with generation time distribution data.

Variation in S phase in synchronous human cell lines

Growth parameters of diploid and trisomic human fibroblasts were determined. The rate of growth of both classes of cells was examined in asynchronous cultures, and diploid and trisomic cells had similar growth rates. Synchronous cultures were developed using simple mitotic selection. The patterns and length of the DNA synthetic period (S phase) were found to be altered in trisomy 21 cells when compared to diploid human or to heteroploid HeLa cells. Early S-phase synthesis was absent or reduced and the overall length of the S phase was extended. However, the trisomic cells have apparently normal rates of DNA chain elongation and normal replicon sizes.

Difference between diploid and aneuploid Chinese hamster cells in replication at mid-S-phase

Following partial synchronization of the heteroploid Chinese hamster cell line V-79 and of normal diploid lung fibroblasts of the Chinese hamster in culture, their DNA replication during S-phase aws compared by means of a BrdU-incorporation/thymidine pulse technique and Hoechst-Giemsa differential staining of metaphase chromosomes. This comparison indirectly shows the S-phase of the heteroploid cells of V-79 to be 2 h shorter than the diploid cell S-phase. When the thymidine pulse is applied to diploid lung fibroblasts at mid-S-phase, differential staining colours metaphase chromosomes a pale blue. Performing the corresponding experiment with V-79 cells, neither a pale blue nor dark red staining is obtained, but rather an intermediate shade, showing prominently dark staining regions in parts. The pause in DNA synthesis observed at mid-S-phase of the diploid Chinese hamster lung fibroblasts seems to be omitted at mid-S-phase of the V-79 cells.

DNA fork displacement rates in synchronous aneuploid and diploid mammalian cells

DNA fork displacement rates were measured in Chinese hamster ovary cells (CHO), human HeLa cells and human diploid fibroblasts. For CHO cells two independent techniques were used: one based on CsCl equilibrium density gradients and the other on 313 nm photolysis of incorporated bromodeoxyuridine (BrdUrd). Both methods indicated that there was no significant variation in fork displacement rates in CHO cells as they progressed through S phase. Asynchronous CHO cultures displayed the same average value (1.0 micron/min) and range of values as found in synchronous cells. In contrast, the rate of DNA fork displacement in HeLa cells, measured by the BrdUrd-313 nm method, increased continuously from 0.8 micron/min in early S to 2.5 micron/min in late S. For human diploid fibroblasts, in early S, the rate was approximately 0.7 micron/min and decreased to a minimum of 0.5 micron/min in mid S. The replication fork displacement rate then increased to a maximum of 0.9 micron/min in late S and declined again before the end of S phase. This pattern of DNA fork displacement rates roughly paralleled the overall thymidine incorporation rate and appears quite different from the patterns found for HeLa and CHO cells.

Cell cycle and the concept of physiological age with special reference to pyruvate kinase activity in WI-38 cells

WI-38 cells were synchronized by mitotic collection and periodically assayed for pyruvate kinase activity. The kinetics of the synchronous cohort were determined by continuous labelling index and by mitotic index. The experimental data were analysed by computer using a state vector model to yield the probability density functions for phase transit times and for cell physiological ages. Pyruvate kinase activity for these cells as a function of physiological age was then examined using the computer model. Considering DNA synthesis, pyruvate kinase activity and mitosis to be markers of physiological age, it was found that a model which assumes that a cohort of synchronized cells desynchronizes irreversibly and uniformly from one age marker to the next is incompatible with the experimental data. For example, the times over which cells entered the S phase were too widely distributed to be consistent with the mitotic index data. Also, for pyruvate kinase activity to be a function of physiological age alone, the cell ages were probably too dispersed to be compatible with the experimental enzyme data. Alternative models for cell physiological ageing are presented, which are compatible with the experimental data.

Isolation of high-rate DNA synthetic cells by con A chromatography

The separation of L1210 cells with columns of Con A-derivatized nylon was investigated. Most of the cells bound to the column irreversibly. The binding was lectin-specific. Cells were pulse labeled with 3H-thymidine and applied to Con A columns. Those cells not binding the columns were enriched in incorporated thymidine compared to the unseparated population. Data is presented which suggests that a small, synchronized fraction of cells synthesizing DNA at a high rate is reduced in Con A-nylon affinity. It is proposed that L1210 cell DNA synthesis is not uniform in rate and that changes in this rate are related to changes in the ability of cells to bind Con A-nylon.

Characterization of the cell cycle of cultured human diploid cells: effects of aging and hydrocortisone

Age-related changes in the cytokinetics of human diploid cells in vitro have been compared in normal cultures and in cultures in which lifespan has been prolonged by the addition of hydrocortisone to the medium. For both cultures, with advancing age the fraction of cells in the actively proliferating pool decreased and the intercellular variation in cell cycle times increased. The average cell cycle time was prolonged during aging due almost entirely to changes in the duration of G1. The duration of S remained constant, while a small delay in G 2 was observed in late passage cells near the end of their lifespan. Although the same pattern of change in proliferative parameters occurred in both control and hydrocortisone-treated cultures, the changes were somewhat delayed in the presence of the steroid. The results are interpreted in terms of several cell cycle models and suggest that the events controlling cell proliferation are sensitive to hydrocortisone modulation during the G1 and possibly the G2 periods.

Quantized generation time in mammalian cells as an expression of the cellular clock

The distribution of possible generation times in mammalian cells does not appear to be continous within the limits of range for each cell type; rather, generation time is quantized in multiples of 3-4 hr. Synchronous cultures of Chinese hamster V79 cells were prepared using manual and automated methods to select and stage mitotic cells. Using synchronous cultures and time-lapse video tape microscopy, it was possible to show that generation times within a population of mitotically selected cells normally disperse in a quantized fashion, with intervals of 3-4 hr occurring between bursts in division. In addition, at temperatures above 37 degrees, V79 cells have a 7.5-8.5 hr modal cell cycle, while at temperatures from 36.5 degrees to 33.5 degrees the modal cell cycle is 11-12 hr long. A survey of the synchrony literature reveals that the tendency to preferred generation times holds between cell lines. The distribution of modal generation times from a variety of different cell types forms a series with a similar interval but with a greater range of values than that observed here for V79 cells. To satisfy the published data and the work presented here, I propose a subcycle, Gq, which has a traverse time equal to the period of the clock. The period appears to be fixed at close to the same value in all mammalian somatic cells. The timekeeping mechanism appears to be temperature compensated, since the time required to traverse Gq is constant at temperatures between 34 degrees and 39 degrees. It is suggested that cell cycle time increases at lower temperatures, lower serum concentration, and high cell densitite because the number of rounds of traverse through Gq increases.

The temporal structure of S phase

DNA synthesis in the S phase of V79 and CHO Chinese hamster cells was examined in detail using an automated system for selection and subculturing of mitotic cells and four different assays for DNA synthesis. Flow microfluorometric (FMF) analysis showed that the selected populations were highly synchronous with few noncycling cells. In CHO cells changes in mean and modal fluorescence in the FMF suggested that DNA content increased in a saltatory fashion with 10-20% of the DNA replicated in early S, 40% in mid S, and 40-50% in late S. Pulse labeling and acid precipitation revealed a repeatable pattern of fluctuations in the rate of isotope incorporation with the maximum rate occurring late in S both V79 and CHO. Autoradiography proved to be the best means of accurately determining the beginning of S phase. Cumulative labeling from mitosis to points in S exaggerated the differences in rate between early and late S, so that significant DNA synthesis in early S might easily be overlooked using this method. In CHO cells DNA-specific fluorescence by the Kissane and Robins assay supported the isotopic incorporation data and the FMF analyses by exhibiting a stepwise increase. In V79 cells, S phase lasts only 5 or 5.5 hr, and consequently the mid S and late S steps in fluorescence are compressed. In V79, greater than 80% of the increase in DNA-specific fluorescence occurred between 4.5 and 7 hr after mitotic selection. In both cell lines, fluorescence in early S phase frequently increased transiently to maximum and then decreased.

Characteristics of proliferative cells from young, old, and transformed WI 38 cultures

Mitotic cells were obtained by a shake off procedure from cultures of normal WI 38 cells at various passage levels, and from SV-40 virus transformed cells. The size of all mitotic WI 38 cells was similar regardless of in vitro age, whereas cells from the monolayer displayed an age-related increase in size. Mitotic transformed cells were similar to normal in size, but no size changes were observed in transformed monolayer cells during serial passage. Ultrastructural studies of mitotic WI 38 cells revealed no consistent change in the numbers of mitochondria or lysosome-like bodies during aging in culture. Mitotic transformed cells displayed numbers of mitochondria comparable to normal cells, but lysosome-like bodies occurred less frequently. Size distribution and structural characteristic are presented in relation to the ability of cells to synthesize DNA and to divide. These results support the contention that aging in WI 38 cultures is characterized by a declining fraction of homogeneous, actively dividing cells, and an increasing fraction of heterogenous nondividers that display senescent changes.

Age distribution of human diploid fibroblasts. A stochastic model for in vitro aging

Variation in the lifespan of mass cultures and clones of human diploid fibroblasts can be explained on the basis of variation in the length of the mitotic cycle. This variation is of biological significance; the intrinsic standard deviation of culture lifespan is equal to about 10% of the mean. We constructed a two-parameter stochastic model based on the following assumptions: the time between successive divisions of a given cell is of random duration; cells divide or lose the ability to divide independently of one another; the probability that a cell can undergo further division is constant up to some maximum number of divisions and zero thereafter. We determined numerically the proportion of nondividing cells and the distribution of cell generations. Samples taken by Monte Carlo means from a hypothetical in vitro population were compared with clonal survival data obtained experimentally. The fit between experimental and theoretical findings was within the range of sampling variation. If we accept our model as being applicable to human diploid cell culture, we can draw the following conclusions: the proportion of dividing cells is an inadequate index of a population's age; even in populations in which almost all cells are still capable of division, a majority of the cells have less than eight generations remaining to them. At each subcultivation the ultimate fate of a culture is determined by the disposition of a relatively small number of "young" cells.