S phase, an evolutionary chromatin condensation state from G1 to G2, in a breast epithelial cell line.

In order to better understand the changes in DNA organization during the cell cycle, we quantified the chromatin texture of breast epithelial cells and followed its evolution through a cell cycle. The diversity of quiescent cell states led us to limit this study to proliferating cell phases, and to choose a cell line with no G0 cells, the MDA AG cell line. We recently developed a methodology for characterizing in situ the cell cycle of breast epithelial cell lines using a cell image processor. This method is based on 15 densitometric and texture parameters computed on individual Feulgen-stained nuclei and on multiparametric analysis of the resulting data. Chromatin pattern assessment is based on nine texture parameters measured from grey-level co-occurrence and run-length section matrices. In the present study, texture parameter computation showed gradual and progressive modifications of nuclear texture. While discrimination of G1, G2 and M phases was possible, we could not discriminate G1 from S and S from G2. The chromatin pattern (defined by these nine parameters) in the G1 and early S phases, on the one hand, and in the late S and G2 phases, on the other hand, were similar. The parameter values of cells in the S phase progressively increased from G1 to G2. Two interphase chromatin condensation states were distinguished in these breast cells: a base state characteristic of a prereplicative stage and a very granular state characteristic of a postreplicative stage. We hypothesized that S cells are a blend of these two states, the evolution of a non-duplicated state toward a duplicated one.     

Cdc6 protein causes premature entry into S phase in a mammalian cell-free system.

We exploit an improved mammalian cell-free DNA replication system to analyse quiescence and Cdc6 function. Quiescent 3T3 nuclei cannot initiate replication in S phase cytosol from HeLa or 3T3 cells. Following release from quiescence, nuclei become competent to initiate semiconservative DNA replication in S phase cytosol, but not in G0 phase cytosol. Immunoblots show that quiescent cells lack Cdc6 and that minichromosome maintenance (MCM) proteins are not associated with chromatin. Competence of G1 phase nuclei to replicate in vitro coincides with maximum Cdc6 accumulation and MCM protein binding to chromatin in vivo. Addition of recombinant Cdc6 to permeabilized, but not intact, G1 nuclei causes up to 82% of the nuclei to initiate and accelerates G1 progression, making nuclei competent to replicate prematurely.     

G0-G1 cell cycle phase transition as revealed by fluorescence resonance energy transfer: analysis of human fibroblast chromatin

In the present study, microspectrofluorometry and digital imaging procedures were used to investigate by fluorescence Resonance Energy Transfer (FRET) analysis the changes of chromatin organization during the transition from G0 quiescent stat to G1 phase. G0 transition is a key event in cell cycle progress depending on the activation of specific genes and the concomitant silencing of others, which both entail spatial chromatin rearrangement. Normal human fibroblasts arrested in G0-phase by culture in low-serum containing medium and stimulated to re-enter G1 by serum addition were used as cell model. To investigate the occurrence and timing of these supramolecular chromatin changes, we estimated the relative FRET efficiency in single cells after double-helical DNA. Hoechst 33258 amd propidium iodide were used as a donor-acceptor dye pair since they exhibit particularly favourable spectral characteristics, that allow the calculation procedure to be semplified. The results of FRET analysis were compared to those of the immunocytochemical labelling of two nuclear proteins (i.e., Ki-67 and statin) whose expression is an established marker of potentially proliferating G1 cells or resting G0 cells, respectively. FRET efficiency was lower in G0 than G1 fibroblasts: this is likely due to higher chromatin packaging in quiescent cells which especially hinders the interaction with the donor molecules less favourable, in terms of relative distance and spatial orientation. FRET efficiency significantly increased shortly (1h) after serum stimulation of quiescent fibroblasts, thus indicating that chromatin is rearranged in parallel with activation of cycle-related gene; it is worth noting that these signs largely preceded the occurrence of immunopositivity for Ki-67, which was detectable only 24h after serum stimulation. FRET-based analyses which already proved to be suitable for studying the overall chromatin organization in differentiated cells, may now be envisaged as a powerful tool for detecting, in single cells, more subtle changes linked to the activation of early cycle-related genes.     

T98G glioma cells have nicks in DNA in quiescent phase

Human glioblastoma-derived cell line, T98G, is arrested in the G1 phase of the cell cycle when serum is deprived. Using this cell line, we investigated the relation between the cell cycle and DNA single-stranded breaks, "nicks," by an in situ nick-translation method. When T98G cells were cultured without serum for 60 h, many small cells with condensed chromatin and scanty cytoplasm appeared. These small cells that were immunohistochemically considered to be in the G0 or early G1 phase had many nicks in DNA. When serum was added, these small cells with nicks disappeared within 1 to 4 h. VP-16, a DNA topoisomerase II inhibitor, delayed the disappearance of these small cells with nicks. This indicated that the action of DNA topoisomerase II on the chromatin is required to repair nicks in T98G glioma cells and to promote the progression from the quiescent to the proliferating phase.     

Cytophotometric study of changes in the structure of nuclear chromatin induced by the oncogenic adenovirus SA7 (C8)

Infection of primary murine embryonic cell cultures by adenovirus SA7 (C8) results in an increase in chromatin condensation Average optical density of Feulgen stained nuclei 24 h following virus absorption increased for G0/1, S, and G2 cells by 16.1, 11.3 and 13.1%, respectively. This phenomenon is associated with the stimulation of proliferation, with an increase of the S cell amount by 50% of the control values and a decrease of average cell nuclei areas in all phases of cell cycle.     

Early effects of chemical carcinogens as compared to induced cell proliferation. II. Automated image analysis

Static automated image analysis was applied to study early variations of chromatin structure in Feulgen-stained liver nuclei from rats injected i.p. with a single dose of dimethylnitrosamine (DMNA), a well known hepatocarcinogen. An increase of nuclear area and a correspondent decrease of average optical density (integrated optical density/area) was observed, as compared with controls, in nuclei from rats treated with 5.4 mg/kg of DMNA. These findings, which were comparable with those induced by partial hepatectomy, indicate the existence in DMNA-treated cells of a chromatin DNA relaxation similar to the G0-G1 transition previously described for human diploid fibroblasts stimulated to proliferate. Because similar results were independently obtained by flow microfluorimetry, it seems reasonable to hypothesize that chromatin decondensation could be a prerequisite for cancer induction.     

Length of human prematurely condensed chromosomes during G0 and G1 phase

Length measurements on C-banded prematurely condensed no. 1 human chromosomes of G0 and G1 lymphocytes, as well as of synchronized G1 HEp cells revealed that (i) no length difference exists between mitotic chromosomes and G0 chromosomes; (ii) 1 h after PHA stimulation a clear increase in length is detectable; (iii) in isolated cases an increase by the factor 5 can be observed during G1; (iv) the increase is significantly less for constitutive heterochromatin than for euchromatin. The possibility is discussed that these conformational changes of chromatin reflect physiological differences, i.e. the rate of RNA synthesis during interphase.     

Distinction between the G0 and the late G1 phase of rat cells in vivo and in vitro with the nuclear QDH-fluorescence pattern

The quinacrine dihydrochloride (QDH) staining and the [3H]thymidine incorporation patterns were simultaneously analyzed in nuclei of rat cells from a proliferating (granulation tissue) and a nonproliferating tissue (liver). Nuclei from freshly isolated and cultured cells of the rapidly proliferating subcutaneous granulation tissue showed a cell cycle-related pattern similar to that previously described with growing fibroblast-like cells in vitro. Nuclei of liver cells in smears from biopsies and in histological sections showed a fluorescence pattern similar to that of serum-deprived arrested G0 cells from established cell lines. Treatment of primary cultured rat hepatocytes with phenobarbital altered their degree of chromatin condensation similar to that seen after treatment of rats in vivo. The data indicate that the QDH staining pattern is an early marker, suitable for detecting the cell cycle-promoting activity of chemicals (e.g., of tumor promoters) in nonproliferating cells from various tissues in vivo and in vitro.     

Polycomb group protein-associated chromatin is reproduced in post-mitotic G1 phase and is required for S phase progression

Polycomb group (PcG) proteins form two distinct complexes, PRC1 and PRC2, to regulate developmental target genes by maintaining the epigenetic state in cells. PRC2 methylates histone H3 at lysine 27 (H3K27), and PRC1 then recognizes methyl-H3K27 to form repressive chromatin. However, it remains unknown how PcG proteins maintain stable and plastic chromatin during cell division. Here we report that PcG-associated chromatin is reproduced in the G(1) phase in post-mitotic cells and is required for subsequent S phase progression. In dividing cells, H3K27 trimethylation (H3K27Me(3)) marked mitotic chromosome arms where PRC2 (Suz12 and Ezh2) co-existed, whereas PRC1 (Bmi1 and Pc2) appeared in distinct foci in the pericentromeric regions. As each PRC complex was increasingly assembled from mitosis to G(1) phase, PRC1 formed H3K27Me(3)-based chromatin intensively during middle and late G(1) phase; this chromatin was highly resistant to in situ nuclease treatment. Thus, the transition from mitosis to G(1) phase is crucial for PcG-mediated chromatin inheritance. Knockdown of Suz12 markedly reduced the amount of H3K27Me(3) on mitotic chromosomes, and as a consequence, PRC1 foci were not fully transmitted to post-mitotic daughter cells. S phase progression was markedly delayed in these Suz12-knockdown cells. The fact that PcG-associated chromatin is reproduced during post-mitotic G(1) phase suggests the possibility that PcG proteins enable their target chromatin to be remodeled in response to stimuli in the G(1) phase.     

Multiparameter geometric and densitometric analysis of the G0-G1 transition of WI-38 cells.

Automated image analyses were performed using Feulgen stained smears of WI-38 cells that were either confluent, or that had received a nutritional stimulus to proliferate 3 hr before collection. These experiments show that it is possible to observe changes in morphometric and densitometric parameters of nuclei that correlate with structural and functional differences in isolated chromatins from quiescent G0 and proliferation G1 cells that have been demonstrated by other means. Scatter plot analyses of the data indicated the presence of nuclear images from the stimulated G1 population that had the same deoxyribonucleic acid content as the confluent G0 cells, but had greater areas, perimeters and horizontal projections and smaller mean free paths, form factors, and average optical densities. Multiparameter cluster analysis permits, even minimally, an objective, model-independent identification of G0 from G1 cells that present an increased nuclear dispersion (i.e., lower average optical density) systematically accompanied by increased nuclear convolution (i.e., lower form factor), both compatible with the reported increase in available binding sites with respect to G0 cells.     

Flow cytometric analysis of G1- and G2/M-phase subpopulations in mammalian cell nuclei using side scatter and DNA content measurements

Several subcompartments of the cell cycle in addition to the G1-, S-, and G2-phases usually observed were identified by simultaneous flow cytometric measurements of ethidium bromide fluorescence and side scatter intensity of cell nuclei. Metaphase cells and very early G1-phase cells (G1A) with low side scatter intensities were discriminated from interphase cells with high side scatter intensities. The reason for the various side scatter intensities was found to be the different structure of metaphase cells and early G1-phase cells due to chromatin condensation as shown by sorting of the respective cell nuclei. The G1A-phase could further be subdivided into two compartments with very low side scatter (G1A1) and intermediate side scatter (G1A2) intensities. Using partially synchronized cells the duration of these subcompartments of the G1-phase could be estimated. The durations of G1A1- and G1A2-phases were found to be about 10 min and 20 min, respectively, compared to the total duration of the G1-phase of about 3 h. Additional flow cytometric measurements of side scatter intensities of cell nuclei provide therefore further information on subcompartments of the G1- and G2/M-phases.     

Cytogenetic effect of low-level 60Co gamma-irradiation of cultured human lymphocytes in the G1 phase of the mitotic cycle

The dose-dependence of the chromosome aberration frequency in human lymphocytes in vitro exposed to 60Co-gamma-radiation at the G1 stage of the mitotic cycle has proved to be unlike that obtained upon exposure of cells at the G0 stage of the cycle. The data obtained are accounted for by partial activation of the repair system at the G1 stage which is attributed mainly to chromatin decondensation.     

The spatial position and replication timing of chromosomal domains are both established in early G1 phase

Mammalian chromosomal domains replicate at defined, developmentally regulated times during S phase. The positions of these domains in Chinese hamster nuclei were established within 1 hr after nuclear envelope formation and maintained thereafter. When G1 phase nuclei were incubated in Xenopus egg extracts, domains were replicated in the proper temporal order with nuclei isolated after spatial repositioning, but not with nuclei isolated prior to repositioning. Mcm2 was bound both to early- and late-replicating chromatin domains prior to this transition whereas specification of the dihydrofolate reductase replication origin took place several hours thereafter. These results identify an early G1 phase point at which replication timing is determined and demonstrate a provocative temporal coincidence between the establishment of nuclear position and replication timing.     

Fate of newly synthesized histones in G1 and G0 cells

We have shown that quiescent cells as well as those in the G1 phase of the cell cycle synthesize histones at a reduced but significant rate. Now, we show that the histones synthesized during G0 and G1 are stably incorporated into nuclei soon after synthesis. Micrococcal nuclease digestion of nuclei isolated from cells in G0 and G1 revealed that the specific histone variants synthesized in these different physiological states are found associated with DNA as nucleosomes. Nucleosomes were separated by polyacrylamide gel electrophoresis in a reducing buffer so that histone spot morphology, particularly that of the H3s was improved.     

Fluorimetric measurements and chromatin condensation patterns of nuclei from 3T3 cells throughout G1

Using two cytological methods based on nuclear morphology, quinacrine dihydrochloride (QDH) staining and premature chromosome condensation (PCC), it has been possible to identify cell cyle positions within G1 of growing and arrested 3T3 cells. The fluorescent intensity of QDH-stained interphase cells appears to decrease as the cells pass from mitosis to S phase. Likewise, the length and thickness of prematurely condensed chromatids can be related to the cells' position within the G1 period. Data are presented that deal with three interrelated topics: (1) We determined by fluorometric measurements of nuclei from 3T3 cells that the visual observation of the decrease in QDH fluorescence during G1 reflects an actual decrease in total fluorescence and not a dispersion of the fluorescent chromatin in a larger nuclear area. (2) We correlated the results obtained by QDH staining with those of PCC on the same cell samples blocked in G1 by different conditions. Serum-starved and contact-inhibited cell nuclei had the highest intensity, hydroxyurea-treated ones had the lowest intensity, while that of isoleucine-deprived cells was in between. The same relative order of G1 positions was obtained based on PCC morphology. Thus, both methods monitor the state of chromatin condensation and can be used to identify cell cycle position within G1.(3) We showed with both methods that the states of chromatin resulting from the various G1 blocking conditions differ from each other.     

Spatial distribution and specification of mammalian replication origins during G1 phase

We have examined the distribution of early replicating origins on stretched DNA fibers when nuclei from CHO cells synchronized at different times during G1 phase initiate DNA replication in Xenopus egg extracts. Origins were differentially labeled in vivo versus in vitro to allow a comparison of their relative positions and spacing. With nuclei isolated in the first hour of G1 phase, in vitro origins were distributed throughout a larger number of DNA fibers and did not coincide with in vivo origins. With nuclei isolated 1 h later, a similar total number of in vitro origins were clustered within a smaller number of DNA fibers but still did not coincide with in vivo origins. However, with nuclei isolated later in G1 phase, the positions of many in vitro origins coincided with in vivo origin sites without further change in origin number or density. These results highlight two distinct G1 steps that establish a spatial and temporal program for replication.     

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus

We determined the folding of chromosomes in interphase nuclei by measuring the distance between points on the same chromosome. Over 25,000 measurements were made in G0/G1 nuclei between DNA sequences separated by 0.15-190 megabase pairs (Mbp) on three human chromosomes. The DNA sequences were specifically labeled by fluorescence in situ hybridization. The relationship between mean-square interphase distance and genomic separation has two linear phases, with a transition at approximately 2 Mbp. This biphasic relationship indicates the existence of two organizational levels at scales > 100 kbp. On one level, chromatin appears to be arranged in large loops several Mbp in size. Within each loop, chromatin is randomly folded. On the second level, specific loop-attachment sites are arranged to form a supple, backbonelike structure, which also shows characteristic random walk behavior. This random walk/giant loop model is the simplest model that fully describes the observed large-scale spatial relationships. Additional evidence for large loops comes from measurements among probes in Xq28, where interphase distance increases and then locally decreases with increasing genomic separation.     

G2 phase chromatin lacks determinants of replication timing

DNA replication in all eukaryotes follows a defined replication timing program, the molecular mechanism of which remains elusive. Using a Xenopus laevis egg extract replication system, we previously demonstrated that replication timing is established during early G1 phase of the cell cycle (timing decision point [TDP]), which is coincident with the repositioning and anchorage of chromatin in the newly formed nucleus. In this study, we use this same system to show that G2 phase chromatin lacks determinants of replication timing but maintains the overall spatial organization of chromatin domains, and we confirm this finding by genome-wide analysis of rereplication in vivo. In contrast, chromatin from quiescent cells retains replication timing but exhibits disrupted spatial organization. These data support a model in which events at the TDP, facilitated by chromatin spatial organization, establish determinants of replication timing that persist independent of spatial organization until the process of chromatin replication during S phase erases those determinants.     

Nuclear architecture,intranuclear DNA distribution,and nuclease digestion

G0, G1, and mammalian cells and nuclei were shortly digested with either micrococcal nuclease or DNAse I, both before and after mild fixation, either before (G0) or after (G1) partial hepatectomy. Cells were Feulgen stained and examined by high resolution light microscopy. In metabolically active G1 nuclei, intranuclear DNA appears organized at least in two distinct domains, whereby, the highly dispersed one is large enough to be detected at the resolution of the light microscope and appears preferentially attacked by limited DNAse I digestion. The action of the enzyme is readily apparent only in the nuclei that are first digested and then fixed. Spectroscopic characterization of the same nuclei reveals that the fixation causes a sizeable removal of proteins, mostly in the soluble chromatin subfraction. Results are discussed in terms of two control levels for gene expression and for higher order DNA structure.