Decrease of DNA synthesis in amniotic fluid cells during the middle part of S-phase revealed by differential chromosome staining after incorporation of BrdU

Multiple subphases of DNA repair and poly (ADP-ribose) synthesis in Chinese hamster ovary (CHO-K1) cells

The two types of DNA synthesis as well as poly(ADP-ribose) biosynthesis were measured simultaneously in synchronized intact populations of CHO cells throughout the duration of S phase. Naturally occurring DNA fragmentation was detected by random primed oligonucleotide synthesis (ROPS assay). Fractions of synchronous cell populations were obtained by counterflow centrifugal elutriation. By gradually increasing the resolution of centrifugal elutriation multiple non-overlapping repair and replication peaks were obtained. The elutriation profile of DNA repair peaks corresponded to the DNA fragmentation pattern measured by ROPS assay. The number and position of poly(ADP-ribose) peaks during S phase resembled those seen in the DNA replication profile. Our results indicate that PAR synthesis is coupled to DNA replication serving the purpose of genomic stability.

Replication of the heterogeneous heterochromatin of the sex chromosomes of Microtus cabrerae

We used bromosubstitution to investigate the mode of replication of different types of heterochromatin located in the sex chromosomes of Microtus cabrerae. Our results clearly show that, although the heterochromatin is late replicating, the replication timing of different types of constitutive heterochromatin is related to their banding properties: R-type heterochromatin replicates before G-type heterochromatin, and this replication is asynchronous in both sex chromosomes. Furthermore, the late replication behaviour of the inactive X may spread to its constitutive heterochromatin. In some cells, a region of the constitutive heterochromatin of the late replicating X spontaneously switches to early replication, which may be related to transcriptional activity. Replication behaviour of the constitutive heterochromatin in the Y chromosome is similar to that of the late replicating X.

Demonstration of replication patterns in the last premeiotic S-phase of male Chinese hamsters after BrdU pulse labeling

Chromosome replication in the last premeiotic S-phase of male mammals has been previously studied by [3H]thymidine autoradiography and by a 5-bromodeoxyuridine (BrdU)/Giemsa technique. We used a recently developed BrdU-antibody technique (BAT) in this study. The following conclusions were drawn: (1) The replication patterns observed are similar to that of somatic cells. (2) The heterochromatin starts replication in early S-phase. (3) The euchromatic part of the X chromosome of the male Chinese hamster replicates together with the autosomes and therefore behaves isocyclicly and not allocyclicly as hitherto assumed. Hence, genetic inactivity of the X chromosome may be brought about by a mechanism different from that in somatic cells.

Replication asynchrony between homologs 15q11.2: cytogenetic evidence for genomic imprinting

Replication kinetics of the Prader-Willi syndrome critical region (15q11.2) was investigated in seven normal healthy adult females using RBG replication bands. Replication asynchrony between homologs 15q11.2 was identified consistently in about 40% of cells in all individuals. It was limited to the stages in which Xp22, Xp11, Xq13 and Xq24/26 were visible in the late-replicating X chromosome. This asynchrony suggested that replication timing overlapped between 15q11.2 and the early replicating R-bands of the late X chromosome in some cells, and that the difference in replication timing between homologs was probably related to genomic imprinting; the latter has been suggested as a pathogenetic basis of Prader-Willi syndrome. As a result of an analysis of the proportions of asynchronous and synchronous cells in each replication stage, two types of cells were deduced providing 1:1 methylation mosaicism of genomic imprinting was assumed. The first type was composed of cells with normal replication in one homolog and delayed replication in the other. The second type was composed of cells with normal replication in both homologs. Our results provide cytogenetic evidence of methylation mosaicism for mammalian genomic imprinting.

BrdU pulse/reverse staining protocols for investigating chromosome replication

By using a reverse Giemsa staining procedure (TT chromatin pale, TB chromatin dark) it is possible to detect replication in metaphase chromosomes with short (approximately 10 min) 5-bromodeoxyuridine (BrdU) pulses. A pulse protocol allows us to consider the question "What is replicating at this point in time?" and we have investigated replication patterns during cycle transit in stimulated human female lymphocytes. A clear-cut demarcation between R-zone early and G-zone late was not found. Instead, whilst replication commences (with a very staggered start) in R-zones, activity soon appears to transgress band boundaries and gives rise to cells with unclassifiable patterns where chromosomes take on a mottled or reticulate appearance. Replication in R-zones dies out leaving a clear G-zone pattern persisting for the remainder of S which terminates with a very staggered finish. When pulse duration is increased (approximately 1 h) the frequency of unclassifiable cells falls and occasional "mixed-pattern" cells appear which have, within the same cell, typical R- and G-zone regions. The existence of such cells indicates that if a mid-S replication pause exists (and the absence of any mid-S wave of pale stained cells suggests that it does not) it does not make exclusive separation between dark R- and G-band zones.

Analysis of chromosome replication by a BrdU antibody technique

Chromosome replication was studied without synchronization in human lymphocyte and amniotic cell cultures visualizing very short 5-bromodeoxyuridine (BrdU) pulses by an immunologic technique (BAT). The findings agree in general with those facts known from earlier BrdU staining techniques. The very high sensitivity of BAT was shown to allow the detection of replication in a band where 1 in 200 nucleotides is replaced by BrdU. The main observations are: though the replication patterns after BAT appear strange the bands correspond to those described by the Paris Conference (1971). At the beginning of the S-phase a stepwise onset of replication in only a subset of R-bands is confirmed. There is a considerable difference in the sensitivity between early and late S (SE and SL) for the detection of BrdU pulses. This difference probably reflects a different spatial arrangement of chromatin in R-bands as compared with G-bands below the level of cytogenetic analysis. The use of short pulses did not reveal any additional subdivision of SE or SL. The correspondence between chromosomal bands and replicon clusters is discussed briefly with respect to the different time they need for replication.

How does inactivation change timing of replication in the human X chromosome?

The kinetics of replication of the inactive (late replicating) X chromosome (LRX) were studied in karyotypically normal lymphocytes and human amniotic fluid cells. Both cell types were successively pulse labeled with 1-h or 1/2-h thymidine pulses in an otherwise BrdU-substituted S phase after partial synchronization of the cultures at G1/S. For the first time with this technique, the entire sequence of replication was analyzed for the LRX from the beginning to the end of the S phase, with special reference to mid S (R-band to G-band transition replication). The inactive X is the last chromosome of the metaphase to start replication, with a delay of 1 or 2 h, after which time a thymidine pulse results in R-type patterns. In mid S, the inactive X is the first chromosome to switch to G-type replication (without overlapping of both types and without any detectable replication pause). Until the end of S, a thymidine pulse results in G-type patterns. To rule out artifacts that might arise by the synchronization of cultures in these experiments, controls were carried out with BrdU pulses and the BrdU antibody technique without synchronization. In the course of replication, no fundamental difference was seen between the two different cell types examined. In contrast to studies using continuous labeling, this study did not reveal an interindividual difference of replication kinetics in the LRXs of the seven individuals studied; thus it is concluded that the inactive X chromosome shows only one characteristic course of replication.

Dynamic G- and R-banding of human chromosomes for electron microscopy

Synchronized human lymphocytes were exposed to 5-bromo-2'-deoxyuridine (BrdUrd) for incorporation in either G- or R-bands. The substituted bands were revealed by monoclonal anti-BrdUrd antibodies disclosed with either gold-labeled antibodies or with the protein A-gold complex. Sharp G- or R-banding, specific for electron microscopy (EM), was obtained. These banding patterns, referred to as GB-AAu (G-bands by BrdUrd using Antibodies and gold [Au]) and RB-AAu (R-bands by BrdUrd using Antibodies and gold [Au]), resemble dynamic band patterns (GBG and RBG) much more than they do morphologic band patterns (GTG and RHG). The G- and R-band patterns allow accurate chromosome identification and karyotyping. An actual karyotype of human GB-AAu-banded chromosomes at the 750 band level, photographed in the EM, is presented. The method produces excellent band separation and band contrast. Variations in band staining intensities were noted and correlated with BrdUrd enrichment. The C-band regions were positively stained after GB-AAu banding while they were negatively stained after RB-AAu banding. Telomeres appeared heterogeneous after GB-AAu banding suggesting that part of the telomeric bands might be late replicating.

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.

Mapping replicational sites in the eucaryotic cell nucleus

We have used fluorescent microscopy to map DNA replication sites in the interphase cell nucleus after incorporation of biotinylated dUTP into permeabilized PtK-1 kangaroo kidney or 3T3 mouse fibroblast cells. Discrete replication granules were found distributed throughout the nuclear interior and along the periphery. Three distinct patterns of replication sites in relationship to chromatin domains in the cell nucleus and the period of S phase were detected and termed type I (early to mid S), type II (mid to late S) and type III (late S). Similar patterns were seen with in vivo replicated DNA using antibodies to 5-bromodeoxyuridine. Extraction of the permeabilized cells with DNase I and 0.2 M ammonium sulfate revealed a striking maintenance of these replication granules and their distinct intranuclear arrangements with the remaining nuclear matrix structures despite the removal of greater than 90% of the total nuclear DNA. The in situ prepared nuclear matrix structures also incorporated biotinylated dUTP into replication granules that were indistinguishable from those detected within the intact nucleus.

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.

Detection of BrdUrd incorporation in mammalian chromosomes by a BrdUrd antibody. III. Demonstration of replication patterns in highly resolved chromosomes

A bromodeoxyuridine antibody staining technique (BAT) was applied for the analysis of human chromosomes of different chromosomal band resolution. For this purpose lymphocyte cultures were synchronized and labeled with bromodeoxyuridine during the second half of the S-phase. Generally BAT was found comparable to GTG banding though some prominent GTG bands and the constitutive heterochromatin exhibit less intense staining with this technique.

Replication time of interspersed repetitive DNA sequences in hamsters

The replication time of 34 hamster genomic DNA segments containing interspersed repeat sequences was determined by probing the cloned segments with nick-translated early- and late-replicating hamster DNA. One-third of these cloned families replicated early, one-third replicated late, and one-third replicated without temporal bias. 19 different inserts from these clones along with the SINE, Alu, and the LINE, A36Fc, were used to probe Southern blots of early- and late-replicating hamster or human DNA. We report long interspersed repeats, LINEs, are selectively partitioned into late-replicating DNA and are often concertedly hypomethylated, while short interspersed repeats, SINEs, are selectively partitioned into early-replicating DNA. For some interspersed repeat families, this partitioning is complete or almost complete. The CCGG frequency is very low in late-replicating DNA. The mammalian chromosome's pattern of early-replicating R-bands and late-replicating G-bands reflects a differential distribution of LINEs and SINEs.

Cytogenetic replication studies with short thymidine pulses in bromodeoxyuridine-substituted chromosomes of different mouse cell lines

In normal diploid fibroblasts of the mouse, 3T3-SV-3T3-, and Meth A-cells, the chromosome replication patterns were studied by a bromodeoxyuridine (BrdU)-labelling technique. SV-3T3 is a subline of 3T3 transformed by SV 40 and Meth A is a permanent cell line from Balb c transformed by methylcholanthrene. The use of 1 h thymidine pulses permits high resolution of the S-phase after partial synchronization of the cells at G1/S in an otherwise BrdU-substituted S-phase. It could be shown that the autosomal heterochromatin of the mouse (Mus musculus) starts replication during the early S-phase (R-band replication), continues while R-band chromatin finishes, and still replicates when G-band chromatin starts. The heterochromatin finishes before the majority of G-bands have been replicated. There is no fundamental difference in the course of chromosome replication between the different cell lines studied here. It is concluded that there are no obligate changes in the course of the S-phase linked to the process of transformation.

Simultaneous production of R-bands and either replication patterns or sister chromatid differentiation

The dye triplet chromomycin/methyl green/DAPI and some related dye combinations were applied to bromodeoxyuridine (BrdU)-substituted and non-substituted chromosomes. In both kinds of chromosome preparations, tri-staining followed by observation at pH 7 resulted in well defined R-bands (excitation wavelength 436 nm) and a mixed DA-DAPI/Q-banding pattern (360 nm). Two approaches have given satisfactory expression both of reverse bands and of the differential BrdU-substitution present in metaphase chromosomes: (1) direct tri-staining at pH 7 and mounting of the preparations at pH 11; or (2) pretreatment of the preparations with Hoechst 33258 plus UV and hot buffer followed by tri-staining and mounting at pH 7. These methods should prove useful for routine chromosome analysis and, in combination with BrdU-labelling, in studies of chromosome structure and replication.

Characterization of chromosome replication during S-phase with bromodeoxyuridine labelling in Chinese hamster ovary and HeLa cells

Chinese hamster ovary (CHO) and HeLa cells were successively pulse labelled at 1-h intervals after the cultures were synchronized at the end of G1 (monitored by flow cytometry). The metaphases analysed afterwards showed R-type replication patterns after 1-h pulses during the early S-phase (SE; from h 1-5 after release) and replication of G- and C-bands in late S-phase (SL: from h 6-8 after release). The transition from SE to SL is abrupt, constituting a sudden switch of replication between different types of chromatin as has been described for human lymphocytes. The differences between these two cell lines and earlier results reported on a V79 Chinese hamster cell line and on normal diploid human and Chinese hamster fibroblasts are discussed.

Uninterrupted DNA synthesis during S-phase in untransformed diploid hamster fibroblasts

Untransformed Syrian hamster fibroblasts in exponential growth were exposed to a pulse of [3H]-thymidine for 5 min, followed immediately by bromodeoxyuridine, and serial samples were taken up to 16 h. Preparations were autoradiographed and stained for replication banding. No cell with replication bands was found without significant [3H]-thymidine uptake, although the extent of uptake varied between sub-phases of S. Thus there is no indication of a total cessation of synthesis at any period during S-phase.

Description of a chromosome replication unit in individual prematurely condensed human S-phase chromosomes

Mammalian chromosome replication was studied by the aid of premature chromosome condensation (PCC). After induction of PCC the sites of DNA replication appear as "gaps" between condensed chromosomal regions. These condensed particles are unineme before and bineme after DNA replication. The two phases are due mainly to the unineme or bineme nature of the particles. During early S-phase almost all particles are unimene, during late S-phase they are bineme and there is only one transitory stage between these two main stages. Premature chromosome condensation was studied in detail on a specific human chromosome 22 which is marked by its heterochromatin constitution. This led to easy identification of these elements in S-phase PCC (S-PCC) preparations. For each stage of the S-phase there was a reproducible pattern of condensed chromosomal particles making up the whole chromosome. The number of these particles was rather limited and a complementary pattern was found in early versus late S-phase. The pattern of early S-PCC corresponded to the banding pattern of G-banded prometaphase chromosomes; the pattern of late S-PCC, to R-banded prometaphase chromosomes. Thus, "gaps" and condensed particles as observed after PCC induction are obviously homologous to chromosome replication units. Replication of constitutive heterochromatin occurred during the very late S-phase. During this stage PCC induction led to condensation of the heterochromatin into several small, highly fluorescent particles.

Mapping of DNAase I sensitive regions on mitotic chromosomes

We have shown that in fixed mitotic chromosomes from female G. gerbillus cells the inactive X chromosome is distinctly less sensitive to DNAase I than the active X chromosome, as demonstrated by in situ nick translation. These results indicated that the specific chromatin conformation that renders potentially active genes sensitive to DNAase I is maintained in fixed mitotic chromosomes. We increased the sensitivity and accuracy of in situ nick translation using biotinylated dUTP and a specific detection and staining procedure instead of radioactive label and autoradiography and now show that in both human and CHO chromosomes, the DNAase I sensitive and insensitive chromosomal regions form a specific dark and light banding pattern. The DNAase I sensitive dark D-bands usually correspond to the light G-bands, but not all light G-bands are DNAase I sensitive. Identifiable regions of inactive constitutive heterochromatin are in a DNAase I insensitive conformation. Our methodology provides a new and important tool for studying the structural and functional organization of chromosomes.

Characterization of Giemsa dark- and light-band DNA

Using synchronized cultures of V79-8 Chinese hamster lung fibroblasts, we either alternately labeled early- and late-replicating DNA, or substituted one of these with bromodeoxyuridine to separate them in CsCl density gradients or to identify the bromodeoxyuridine-containing chromosome bands by fluorescence microscopy. The Giemsa light R bands were shown to replicate in the first half of S phase, and the dark G bands were shown to replicate in the last half of S phase. S phase was bimodal, with a distinct pause in the rate of DNA synthesis that separated the period of R-band DNA synthesis from that of G-band DNA synthesis. G-band DNA was found to be 3.2% richer in AT than R-band DNA. Surprisingly, G- and R-band DNA appeared equally transcriptionally active in that alternate labels in chromatin were digested with the same kinetics by DNAase I, and in reassociation experiments, total poly(A)+ RNA drove nick-translated G- and R-band DNA probes similarly. G- and R-band DNA also reassociated with identical kinetics, demonstrating that they contain equal proportions of all kinetic-complexity classes of sequences.

High resolution replication patterns of the human Y chromosome. Intra- and interindividual variation

Replication studies on prophasic human Y chromosomes reveal 4 early replicating segments in the euchromatic portion. The distal segment of Yp replicates first. After replication of the euchromatic part is almost finished 3 to 5 segments start replication in the heterochromatic portion of Yq. These segments exhibit considerable intraindividual variation with respect to the origin of onset of replication. While the location of these bands--once they are differentiated--is fixed within one individual, the number of these bands varies interindividually.

Replication variants of the human inactive X chromosome. I. Variability within lymphocytes of single individuals

The sequence of DNA replication was studied within the inactive X chromosome in human lymphocytes, by means of the FPG method. Several variants of the replication sequence were found. The number of variants in the cells of a single donor exceeded 2 in each of the 4 normal individuals studied. The phenomenon is discussed with respect to the regulation of DNA synthesis and to the cell differentiation process.

Asynchrony in late replication between homologous autosomes in primary cultures of Chinese hamster fibroblasts

Asynchronies in late replication of the autosomal chromosome pair No. 5, and to some extent of pair No. 4, were found after thymidine pulse labeling cultures of partially synchronized Chinese hamster lung fibroblasts from nine to nine and a half hours and from nine and a half to ten hours after block removal. In contrast to this, no asynchrony could be detected in the replication of homologous autosomes after continuous labeling for the last two hours of the S-phase. - G-banding and C-banding revealed no differences between the homologous autosomes. - These findings indicate that besides the known form of asynchronous replication in mammalian cells during S-phase on the chromosomal level, there also exists an asynchronous replication between homologous autosomes of the same complement.

Cytological sub-division of S-phase in the Syrian hamster (Mesocricetus auratus)

Using BrdU/Hoechst 33258/Giemsa methods for detecting replicating chromosome bands, a method is described by which the DNA synthesis phase may be sub-divided on the basis of distinctive patterns displayed by certain chromosomes.--Applied to asynchronous populations successively sampled through one cell cycle, cells in S can be "unscrambled" and replaced in their correct time sequence.--This helps to overcome the sampling-time variable inherent in such populations, and allows a clearer picture of the progression of events both qualitatively and quantitatively.

Two phases of DNA replication in human cells

The course of DNA synthesis in the chromosomes was studied in synchronized human lymphocyte cultures, by means of the BrdU-Hoechst-Giemsa method. In comparing replication patterns and G-banding it was found that with regard to banding the process of DNA replication can be divided into two separate phases, an "early replication period" which is characterized by DNA synthesis in R bands of the autosomes and active X chromosome, and a "late replication period" which concerns the G-positive regions of the autosomes and all the bands of the heterochromatic X and Y chromosomes. No overlapping was found between the two phases mentioned. The possible role of regulatory mechanisms was discussed.

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.

Demonstration of replication patterns corresponding to G- and R-type banding of chromosomes after partial synchronization of cell cultures with BrdU or dT surplus

A standard protocol is reported for the highly efficient demonstration of replication patterns corresponding to R-type and G-type banding.

Comparison of thymidine, fluorodeoxyuridine, hydroxyurea, and methotrexate blocking at the G1/S phase transition of the cell cycle, studied by replication patterns

Cultures of human amniotic fluid cells and fibroblasts were temporarily blocked by the replication inhibitors thymidine (dT) surplus, fluorodeoxyuridine (FdU), hydroxyurea (HU), or methotrexate uridine (MU). The respective arresting point at G1-S transition and the homogeneity of the blocked cell population were determined by means of BrdU replication patterns. Most variation of patterns were found after HU. After MU, cells were arrested before the onset of replication, while with dT surplus of FdU an arresting point in early S seemed more likely.