Analysis of DNA replication patterns of human fibroblast chromosomes: the replication map

Visualization of DNA replication sites in mammalian nuclei

DNA replication takes place at discrete sites in the cell nucleus, named replication foci. The spatial arrangements of these foci change in the course of S phase in a temporally regulated and reproducible fashion forming five distinct and highly conserved replication patterns. The organization of nuclear replication sites can be studied by electron and light microscopy techniques. This chapter describes several procedures for detection of replication foci in mammalian nuclei via indirect immunofluorescence microscopy.

Nuclear morphology during the S phase

In order to evaluate at the ultrastructural level the chromatin arrangement during the S phase of the cell cycle, the detection of Bromodeoxyuridine (BrdU) by immunogold has been performed in synchronized 3T3 fibroblasts, regenerating liver, and Friend Leukemia Cells (FLC). After a 5-minute BrdU pulse, this label is detected in 10-nm-wide fibers, organized as lacework and assumed to be replication units. In the early part of the S phase, DNA replication units are localized exclusively in the dispersed chromatin domains far from the nuclear envelope. In the middle S, replication occurs at the border between condensed and dispersed chromatin and, finally, in late S, it mainly occurs in perinuclear heterochromatin regions. After replication, the 10-nm fibers can condense in heterochromatin without translocation. Chromatin is highly dispersed in early S and computer image analysis shows an increase in condensed chromatin areas ranging from 13 to 18% at the end of the S phase with a temporal and morphological pattern of distribution characteristic for each cell type. Scanning transmission electron microscopy demonstrates a regular and repetitive structure of dispersed chromatin, represented by a ring-like arrangement of the 10-nm fibers; assuming the same spatial distribution, gold particles that identify incorporated BrdU confirm this organization. By evaluating the organization and the distribution of DNA replication units during S phase, the results suggest that DNA replication occurs at a nucleosomal-like fiber level and that replicating enzymes machinery moves over a fixed template.

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.

Sequence of DNA replication in Macaca fuscata chromosomes: an outgroup for phylogenetic comparison between man and apes

The relative replication times of every band in the standardized 300 band G-band idiogram of the chromosomes of the Japanese macaque are presented, and compared to the human sequence. Many chromosomes thought to be homologous between Macaca fuscata and man on the basis of standard chromosome banding and gene mapping show a conservation of the replication sequence. Other supposed chromosomal homologies between these two species show no good correspondence, and the replication sequence data suggest that these chromosomes have been subject to complex rearrangements. The replication sequence data also point to possible additional chromosomal homologies between man and M. fuscata. Asynchrony in replication time between homologues from the same cell may also be evolutionarily conserved, because these species share a number of asynchronous homologous bands. Replication band sequence data can provide significant information for comparative cytogenetics. However, usually only the full replication R- or G-band pattern has been used for interspecific comparisons. The dynamic sequence data presented here determine the replication time of every band in the karyotype, and provide a quantitatively and qualitatively more sensitive tool to characterize chromosomes. Such data could provide valuable new information on which to make phylogenetic reconstructions, and shed light on the relationship between chromosome change and evolutionary process. Finally, the M. fuscata replication sequence presented here will provide a necessary foundation for future comparisons between apes and man.

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.

Cell cycle studies in chorionic villi

We have studied the cell cycle of cells obtained from chorionic villi in direct and culture preparations by incorporation of the thymidine analogue BrdU to produce late-labelling or sister chromatid differentiation patterns. We have, therefore, been able to estimate the duration of the cell cycle and, more specifically, the length of some of its phases. While results for chorionic villus sample cells in culture resembled those obtained for fibroblasts, data for the spontaneously dividing trophoblastic cells in direct preparations were different. Villi exposed to BrdU immediately after sampling showed a slight delay in the incorporation of the analogue and a lower percentage of labelled cells compared to villi treated after an overnight incubation, probably due to a temporary effect of the sampling technique. Results from semi-direct protocols suggest that cells have a G2 of no more than 4 h, and a mid-S phase of 10-16 h. The G1 period is very variable. After 48 h incubation with BrdU, only 4% of cells reach their second generation, whereas this percentage increases up to 70% after 72 h, indicating that under these experimental conditions most cells have a cell cycle of approximately 36 h. The average number of sister chromatid exchanges was similar in both direct preparations and cultures: 5.2 +/- 2.1 SCE per cell.

Cytological evidence of defective template in the fragile X chromosome

In cells of fragile X patients, the changed X segment may appear as a poorly staining region or a gap, or as a deletion, involving one or both chromatids. To find out whether the fragile site represents an incompletely replicated DNA sequence, as has been suggested recently, we analyzed the four chromatids of methotrexate-induced endoreduplicated fragile X chromosomes. Our main observations were: (1) a deleted chromatid was never internal to a poorly staining one; (2) an endoreduplicated X chromosome with a fragile site never included a normal chromatid. These results can be explained by assuming that DNA at the fragile site, when replicated in the presence of methotrexate, may undergo defective replication and give rise to improperly packaged chromatin, appearing as a chromatid with a poorly staining region or a gap in the following metaphase. The same DNA may fail to function as a template in the following S-phase and give rise to a chromatid with a single-stranded segment, appearing as a deleted chromatid in the following metaphase.

Replication kinetics of X chromosomes in fibroblasts and lymphocytes

The kinetics of replication for early and late replicating X chromosomes in karyotypically normal fibroblasts and lymphocytes was studied using terminal bromodeoxyuridine (BrdU) treatment followed by Hoechst/light/Giemsa staining. Although the order of band appearance differs between the two tissues, the programme (order and interval between band appearances) for early replicating bands (dark R-bands) is identical in the two homologues. This is probably also the case for later replicating bands (dark G-bands) though the criteria for determining mean band appearance times are less reliable for these bands when terminal BrdU treatment is used. This means that the late X has a delayed start but thereafter proceeds at the same pace as its early counterpart.

Replication of X chromosomes in complete moles

DNA replication patterns of X chromosomes in complete hydatidiform moles were studied using cultured fibroblasts from three 46,XX moles resulting from duplication of a haploid sperm, and from a 46,XY mole originating from dispermy. Control cultures included skin fibroblasts from an adult woman and a female fetus as well as PB lymphocytes from an adult woman. Cultures were treated with 5-bromo-deoxyuridine for the last 2-4 h of the S phase, and the chromosome slides prepared were stained by the Hoechst 33258-Giemsa procedure. Each of the three XX moles studied revealed one early-replicating and one late-replicating X chromosomes, while the XY mole revealed one early-replicating X chromosomes. DNA replication patterns of molar X chromosomes were similar to those of adult and fetal fibroblasts, but different from those in adult lymphocytes. These findings indicate that DNA replication kinetics of molar fibroblasts are tissue-specific rather than origin- or developmental-stage specific.

Analysis of the DNA replication pattern of a translocation (tX/X, qter----p221::p223----qter) chromosome in leukocyte and fibroblast cultures

The results of a detailed analysis of DNA replication in a late replicating tX/X chromosome (qter----p221::p223----qter) are reported. The chronology of DNA replication has been analyzed by comparing (a) the replication patterns of each of the two moieties of the translocation chromosome in different cells and (b) the two moieties with each other in the same cell. The study has been done on leukocyte and fibroblast cultures after BUdR incorporation. A comparison with the late replication pattern of the normal X chromosome has also been done.

Cytological subdivision of the S phase of human cells in asynchronous culture

A method is described for subdividing S phase cells in asynchronous cell cultures on the basis of replication band patterns produced in chromosomes by bromodeoxyuridine incorporation. The criteria used for cell classification are objective, requiring the presence or absence of specific bands on particular chromosomes, and therefore lead to subdivisions amenable to quantitative analysis and for comparative purposes. Two schemes are given: key 1, based on bands in chromosomes 2 and 5, leads to five sub-phases; and key 4, based on bands in chromosomes 3 and 4, leads to four sub-phases. The order of the sub-phases, though not their relative durations, is identical in the six primary cell cultures (four fibroblast and two lymphocyte) tested. The technique provides for a detailed study of the programme of chromosome replication in normal and abnormal cells which, in time, should produce new criteria for diagnostic purposes.

Detailed cell cycle analysis in human lymphocytes; application to gamma-irradiated cells

A method based on BrdU incorporation for analyzing in detail the kinetics of the cell cycle is described. The S phase has been subdivided into five subphases, each recognizable by their BrdU incorporation pattern at metaphase. The method can be useful for the study of abnormal cell cycles, and may have particular application in mutagenesis studies concerning the various subphases of the S phase, without using synchronization techniques. An application of the method is described, showing that gamma-irradiation, during the course of the S phase, leads to a lack of cells which were in early S phase at the time of irradiation. This finding can be related either to a higher lethality at this stage of the cell cycle or to a delay in completion of DNA replication after irradiation.

A simple and reliable method of chromosome banding for prenatal cytogenetics using a bromodeoxyuridine pulse

An extremely simple, fully defined and reliable technique for banding chromosomes in situ is described. The method uses a pulse of bromodeoxyuridine to produce replication pattern banding complete with G- and C-type banding in the same karyotype. This enables immediate resolution of problems otherwise requiring extra subculturing and the application of conventional banding techniques. The value of routine chromosome banding in prenatal cytogenetics using such an economical technique is discussed.

Chromosomal replication asynchrony of a human breast carcinoma cell line. I. studied by continuous BrdU incorporation and G-banding analysis

Continuous BrdU incorporation and the Giemsa staining technique were used to study the cell cycle kinetics of a human breast tumor cell line. It was found that the interchromosomal replication pattern of the neoplastic cell was significantly different from that of normal cells in two respects. First, the pattern is highly asynchronous; within a single cell there are chromosomes at different replication cycles; that is, some chromosomes complete their DNA replication before others begin. Second, the replication schedule for the chromosomes, as identified by superimposing the BrdU-Giemsa technique on the trypsin G-banding technique, is relatively consistent within the cell line but differs from that of normal cells. Some chromosomes that replicate late in normal human lymphocytes and fibroblasts replicate early in this cell line. In contrast to the unusual interchromosomal replication pattern, gross analysis of the intrachromosomal replication schedule shows no apparent difference from that reported for normal cells. The asynchrony phenomenon reported here may be associated with the etiology of aneuploidy in neoplasia.

DNA replication sequence in a dicentric (functionally monocentric) X chromosome formed by the joining of two X chromosomes at region p22

In this study we used densitometry to evaluate DNA replication kinetics in a rearranged chromosome formed by the joining of two X chromosomes at region p22. No 45X mosaicism is present in peripheral blood or fibroblast cultures. The patient has primary amenorrhea, short stature, and gonadal dysgenesis. The sequence of replication in the majority of cells is p11, q11, q13, q22-24, q12, p22, q26, q28, q27, q25, and p21, q21. Thus p11 is the earliest region to replicate, and q21 is the last. In 66% of 127 cells analyzed, the replication pattern is asymmetric, and bands q12, q26, and q28 are most likely to be out of phase on the two sides of the breakpoint. We find that band p22 has a delay of replication compared to an abnormal X derived from two X chromosomes joined at the q23 region previously reported by us. Structural rearrangement may therefore delay replication in the region of the break.

Kinetics of DNA replication in a dicentric X chromosome formed by long arm to long arm fusion

Utilizing the 5-bromo-deoxyuridine (BrdU) incorporation technique, we have recently studied the DNA replication kinetics in a dicentric X chromosome, formed by long arm-to-long arm fusion at band q23, for a 16-year-old black female with primary amenorrhea. The patient has a karyotype 45,X/46,X,dic(X)(q23). In the buccal smear the presence of X chromatin was found in 33% of the cells examined. The Barr bodies are large and 21% of them are bipartite. DNA replication studies were performed on the patient's lymphocytes by the thymidine pulse (T-pulse) method and confirmed comparatively by the BrdU pulse (B-pulse) method. The results indicate that the dicentric X chromosome is always late-replicating. The replication pattern is symmetric on both sides of the breakpoint and the replication sequence is, in order, p11, p22, q1(1-3), q22, q23, p21, and q21. This finding is comparable to those of other investigators and supports the theory that there exist two inactivation centers in the dicentric X chromosome, located on or near the q21 band.

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.

A deleted extra chromosome 22 identified by DNA replication banding

The identification of a deleted extra chromosome 22 by means of the DNA replication banding pattern is reported. The characteristics of DNA replication banding, its advantages and superiority in chromosome identification are described.

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.