Detection by density equilibrium centrifugation of recombinant-like DNA molecules in somatic mammalian cells

Disparity of gene conversion in frameshift mutants located in locus b2 of Ascobolus immersus

The frequency of conversion and the disparity in the direction of conversion were studied for six frameshift mutants lying in locus b2 of Ascobolus immersus and giving more 2 wild type:6 mutant (2+6m) than 6 wild type:2 mutant (6+2m) aberrant asci (type B). The frequency of conversion decreased from left to right in the locus. The disparity steadily increased from left to right and then reached a plateau. Twenty-two frameshift mutants giving more 6+2m than 2+6m aberrant asci (type A) and closely linked to three type B mutants were also studied; they showed the same frequency of conversion and the same disparity (but in the opposite direction) as the type B mutant to which they are linked. The polar variation of both the frequency of conversion and the disparity as a function of position were expected on the basis of a previous study of 15 mutants giving postmeiotic segregations and located in locus b2. This variation is assumed to reflect the existence of a preferential region for the initiation of hybrid DNA (HDNA) during recombination and a duality in the distribution of this HDNA, with preponderant asymmetrical HDNA near the starting point and preponderant symmetrical HDNA farther from it.

Analysis of intrachromosomal homologous recombination in mammalian cell, using tandem repeat sequences

In all the organisms, homologous recombination (HR) is involved in fundamental processes such as genome diversification and DNA repair. Several strategies can be devised to measure homologous recombination in mammalian cells. We present here the interest of using intrachromosomal tandem repeat sequences to measure HR in mammalian cells and we discuss the differences with the ectopic plasmids recombination. The present review focuses on the molecular mechanisms of HR between tandem repeats in mammalian cells. The possibility to use two different orientations of tandem repeats (direct or inverted repeats) in parallel constitutes also an advantage. While inverted repeats measure only events arising by strand exchange (gene conversion and crossing over), direct repeats monitor strand exchange events and also non-conservative processes such as single strand annealing or replication slippage. In yeast, these processes depend on different pathways, most of them also existing in mammalian cells. These data permit to devise substrates adapted to specific questions about HR in mammalian cells. The effect of substrate structures (heterologies, insertions/deletions, GT repeats, transcription) and consequences of DNA double strand breaks induced by ionizing radiation or endonuclease (especially the rare-cutting endonuclease ISce-I) on HR are discussed. Finally, transgenic mouse models using tandem repeats are briefly presented.

Benzo[a]pyrenediol-epoxide induces loss of heterozygosity in Chinese hamster ovary cells heterozygous at the aprt locus

Benzo[a]pyrenediol-epoxide (BPDE), a metabolite of the ubiquitous environmental carcinogen benzo[a]pyrene (B[a]P), has been implicated as a point mutagen. However, as mutational events other than point mutations are also often associated with cancer, we have investigated whether BPDE can induce other classes of mutation. This was done by analyzing mutation at the aprt and hprt loci, both in hemizygous (D422) and heterozygous (D423) Chinese hamster ovary (CHO) cell strains. Southern blotting analysis indicated that BPDE is not an effective producer of either deletions or insertions in the hemizygous environment. The analysis of mutation in the aprt heterozygote was done to investigate the frequency of loss of heterozygosity (LOH) events following BPDE treatment. Using PCR to produce an artificial restriction fragment length polymorphism in the functional aprt allele, BPDE was found to induce LOH in about one-quarter of the mutants recovered. While the precise mechanism of this phenomenon remains obscure, it is likely to have important implications, since similar events involving homologous recombination in somatic cells may have an impact in tumorigenesis.

Fate of DNA lesions that elicit sister-chromatid exchanges

Using 3-way differential staining (TWD) of sister chromatids, the fate of DNA lesions involved in sister-chromatid exchange (SCE) formation was determined in murine bone marrow cells in vivo, after treatment with either mitomycin C (MMC) or cyclophosphamide (CP). Both MMC (2.6 mg/kg b.w.) and CP (7 mg/kg b.w.) induced an SCE frequency near the expected in the 2 subsequent cell divisions, but the frequency of SCE occurring at the same locus in successive cell divisions was substantially lower than expected. The results are compared with previous data obtained after exposure to gamma-rays. A model of SCE induction is proposed.

Effect of DNA damage on stable transformation of mammalian cells with integrative and episomal plasmids

The efficiency of stable transformation of human cells by integrative (non-replicating) plasmids carrying a selectable gene has been shown to be markedly enhanced by the introduction into the plasmid DNA of bulky damage, such as cyclobutane pyrimidine dimers or psoralen photoadducts. Enhanced transformation (ET) occurs in all human cells tested, including DNA repair-deficient cells from the hereditary syndrome xeroderma pigmentosum, but significantly less, if at all, in rodent cells. ET has been observed with a variety of integrative plasmid constructs, suggesting the generality of the phenomenon; as expected, ET is due to an increase in the number of cells carrying integrated plasmid sequences. In contrast to integrative plasmids, stable transformation by episomal (autonomously replicating) plasmids derived from the Epstein-Barr virus is only depressed by the introduction of photoproducts; furthermore, pronounced inactivation of transformation mediated by episomal plasmids becomes apparent in xeroderma pigmentosum cells. Altogether, these results suggest that DNA damage increases the probability of stable insertion of heterologous non-replicating DNA into human chromosomes. Moreover, the differential sensitivity to DNA damage of human cell transformation mediated by integrative versus episomal plasmids suggests caution in using such assay to measure host cell reactivation capacity; processing of DNA damage in mammalian cells might differ significantly between intra- versus extra-chromosomal DNA. Since ET may be induced by damage outside the selectable gene carried on integrative plasmids, we propose a model that involves local disruption of chromatin structure by helix-distorting DNA lesions flanking actively transcribed sequences; alternatively, reorganization of such altered DNA structure might be favored by the presence of topoisomerase-like activities in the proximity of active genes. Because ET can also be induced by DNA damage to the recipient cells, it is speculated that similar mechanism(s) might be involved in the generation of other types of non-homologous DNA recombination in damaged human chromosomes, including oncogenic cell transformation mediated by integrative DNA viruses.

The effect of X-rays and ultraviolet light on DNA-mediated gene transfer in mammalian cells

The uptake, expression and genomic integration of exogenous DNA during DNA-mediated gene transfer are poorly understood in mammalian cells. We studied the effects of ionizing radiation and u.v. light treatments on recipient cells during gene transfer experiments. We found that both X-rays and u.v. light stimulate pSV2-gpt DNA transfer into V79 Chinese hamster cells and they are equally effective for an equi-cytotoxic dose. This result was observed with irradiation both before and after the period of DNA precipitate overlay of the recipient cells. The stimulation of DNA transfer was approximately proportional to dose for both types of radiation. The effect was significantly enhanced using chronic, rather than acute, radiation treatments. The optimal expression time to observe stimulation of DNA transfer, however, differs for the two radiation types. A possible model for DNA-mediated gene transfer, incorporating this result, is discussed.

Kinetics of recombinational hybrid formation in X-irradiated mammalian cells: a possible first step in the repair of DNA double-strand breaks

It is known that mammalian cells repair X-ray-induced double-strand breaks (DSB). The mechanism of this repair is, however, as yet unknown but it is thought that the repair may involve recombination between homologous DNA strands. We have investigated the presence and kinetics of occurrence of recombinational molecular intermediates or 'heavy-heavy' (HH) hybrids in DNA of X-irradiated mouse Ehrlich ascites tumour cells unifiliarly substituted with bromodeoxyuridine. Purified DNA from density-labelled cells was analysed using isopyknic CsCl density centrifugation. After rebanding of the high-density material, the relative amount of HH-hybrid material was determined. When the cells were incubated after X-ray exposure, hybrids accumulated with an apparently biphasic kinetic; first a rapid accumulation directly after irradiation followed by a second, more slowly appearing peak. When DSB repair was inhibited by the nucleoside analogue 9-beta-D-arabinofuranosyladenine (ara-A), a powerful DNA polymerase inhibitor, the kinetics of the HH-hybrid formation were similar to those during the incubation after X-irradiation without ara-A. We interpret this as indicating that the first step in repair of DSB i.e. hybrid formation, occurs in the absence of DNA synthesis as predicted by the Resnick model of DSB repair. In an experiment in which the ara-A was washed away from the irradiated cells after 8-h treatment with the drug and replaced by fresh growth medium, so allowing DSB to repair, a similar HH-hybrid kinetic response was found to that occurring directly after irradiation in the absence of ara-A. The reasons for this are not yet clear. In this case, however, the response of the ara-A-treated cells after X-irradiation was much stronger than that in the untreated cells where only approximately 20% of the DSB remained. These kinetic results which show a temporary appearance of HH hybrids, indicate that a net exchange of genetic material does not take place; they therefore lend support to the postulated recombinational model of Resnick in which a temporary exchange between homologous DNA strands takes place during DSB repair.

Homologous recombination in mammalian cells mediates formation of a functional gene from two overlapping gene fragments

Chinese hamster cells with a lesion in the CAD gene (cell line Urd-A) require exogenous uridine to survive. Uridine prototrophs could be isolated after introducing two recombinant plasmids containing overlapping fragments of a cloned Syrian hamster CAD gene. In contrast, no uridine prototrophs were obtained after introducing a plasmid containing only one of the two overlapping fragments. DNA restriction analysis showed that the prototrophic transformants contain a functional CAD gene which was formed by a recombination event in the overlapping region of the two clones. Most of the recombination events involved homologous exchanges, and some of them apparently were reciprocal. In situ hybridization analysis revealed that the donated sequences were integrated at a single chromosomal site which was different in each transformant. These results demonstrate the existence of a recombination system(s) in mammalian cells that can catalyze homologous exchanges. Recombination between donated sequences is a means by which this system can be characterized and also utilized for the production of novel gene fusions.

Unstable high molecular weight inverted repetitive DNA in human lymphocytes

About 1% of newly synthesized DNA from PHA-stimulated human lymphocytes can be isolated as large (up to 90 kilobase pairs) double stranded fragments that resist sequential alkali and heat denaturation steps but are not closed circular. By electron microscopy about 1% have single-strand hairpin loops at one end and therefore present inverted repetitive sequences (IR-DNA). Most of the remainder have a blunt-appearing double-strand terminus at both ends (78%) or one end (18%). Indirect evidence indicates that these also are inverted complementary structures with terminal hairpin loops too small to be visualized: (1) Treatment with either a 5' or 3' single-strand exonuclease generates essentially only fragments with a single strand at one end; (2) with partial denaturation, the number of fragments with identifiable single-strand hairpin loops increases (to about 20%); (3) after S1 nuclease digestion, greater than 95% can be fully heat denatured. Cot analysis indicates that these fragments are derived from dispersed sites throughout the genome. Up to 25% of DNA released from lymphocytes during growth similarly resists denaturation, and released DNA and IR-DNA are both enriched in the same set of repetitive sequences. Thus at least a portion of IR-DNA appears to be unstable.

Effect of UV-irradiation on DNA replication of the parvovirus minute-virus-of-mice in mouse fibroblasts

The effect of UV-irradiation on the conversion of the single-stranded DNA of the parvovirus Minute-Virus-of-Mice (MVM) to duplex Replicative Forms (RF) was studied after infection of mouse A9 fibroblasts. UV-irradiation of the virus prior to infection of unirradiated cells resulted in a dose-dependent, single-hit, inhibition of RF formation. Restriction fragment analysis indicated that this inhibition could be ascribed to the introduction of absolute blocks which prevent elongation of the newly synthesized complementary strand. Cell exposure to UV-light prior to infection with UV-irradiated MVM enhanced the fraction of input viral DNA which was converted to RF. This enhancement required de novo protein synthesis during the interval between cell irradiation and virus infection. These results suggest that DNA replication constitutes a target in the viral life cycle that leads to the UV-enhanced Reactivation of virus survival, however, they do not permit us to identify the step of RF formation which is enhanced in UV-pretreated cells.

Mechanisms of tolerance to DNA lesions in mammalian cells

In recent years it has become clear that different pathways are involved in the process of removing lesions from DNA. In spite of a continuous surveillance of the genetic integrity by repair enzymes, quite often lesions are not eliminated before the portion of the genome where they have been inserted is used for DNA replication or transcription. Actually, the number of unexcised lesions a cell can tolerate without significantly losing its capacity to reproduce is surprising. As an example, human fibroblasts from certain patients with the genetic disease xeroderma pigmentosum (XP)† are virtually unable to excise pyrimidine dimers, the major DNA lesion produced by short-wavelength UV light.

Postreplication repair in Saccharomyces cerevisiae

Postreplication events in logarithmically growing excision-defective mutants of Saccharomyces cerevisiae were examined after low doses of ultraviolet light (2 to 4 J/m2). Pulse-labeled deoxyribonucleic acid had interruptions, and when the cells were "chased," the interruptions were no longer detected. Since the loss of interruptions was not associated with an exchange of pyrimidine dimers at a detection level of 10 to 20% of the induced dimers, we concluded that postreplication repair in excision-defective mutants (or leaky mutants) does not involve molecular recombination. Pyrimidine dimers were assayed by utilizing the ultraviolet-endonuclease activity in extracts of Micrococcus luteus and newly developed alkaline sucrose gradient techniques, which yielded chromosomal-size deoxyribonucleic acid after treatment of irradiated cells.

Correspondent reaction of mitotic recombination in yeast and sister chromatid exchange in human lymphocytes

In the lower eukaryote Saccharomyces cerevisiae, 4,5,6-trichloro-2-(dichlorophenoxy)phenol and acridine orange cause different specific genetic alterations, either gene mutations or recombinations. These specific effects were used to characterize the mechanism of sister chromatid exchange (SCE) formation in human lymphocytes. Assuming that genetically active substances have comparable effects in lower and higher eukaryotes, the observations provide indirect evidence for a connection between induced mitotic recombination in yeast and SCEs in human lymphocytes and suggest that SCEs may be the consequence of a repair process.

Yeast chromosomal DNA molecules have strands which are cross-linked at their termini

The microbial eukaryote Saccharomyces cerevisiae has 18 chromosomes, each consisting of a DNA molecule of 1 x 15 x 10(8) daltons (150 to 2,300 kilobase pairs). Interstand cross-links have now been found in molecules of all sizes by examining the ability of high molecular weight DNA to snap back, i.e., to rapidly renature after denaturation. Experiments in which snap back was assessed for molecules broken by shearing indicate that there are probably two cross-links in each chromosome. Evidence that the cross-links occur at specific sites in the genome was obtained by treating total chromosomal DNA with the endonuclease EcoRI which cleaves the yeast genome into approximately 2,000 discrete fragments. Cross-link containing fragments were separated from fragments without cross-links. This purification resulted in enrichment for about 18 specific fragments. To determine whether the cross-links are terminal or at internal sites in chromosomal DNA, large shear-produced fragments were examined by electron microsopy. With complete denaturation few fragments exhibit the X-shaped single strand configuration expected for internal cross-links. When partially denatured fragments were examined some ends had single strand loops as expected for (AT-rich) cross-linked termini. We propose that a duplex chromosomal DNA molecules have cross-linked termini. We propose that a duplex chromosomal DNA molecule in this eukaryote consists of a continuous, single, self-complementary strand of DNA. This structure has implications for the mechanism of chromosome replication and may be the basis of telomere behavior.

Satellite DNA and heterochromatin variants: the case for unequal mitotic crossing over

Variations of constitutive heterochromatin (heteromorphisms) appear to be a general feature of eucaryotes. A variety of molecular and cytogenetic evidence supports the hypothesis that heteromorphisms result from unequal double-strand exchanges during mitotic DNA replication. Constitutive heterochromatin consists of highly repeated DNA sequences that are not transcribed. Thus, heteromorphisms are tolerated without overt phenotypic effect. Several of the highly repeated DNAs that comprise constitutive heterochromatin have been shown to contain site-specific endonuclease recognition sequences interspersed at regular intervals dependent upon nucleosome structure. These interspersed short repeated sequences could mediate unequal crossovers, resulting in quantitative variability of constitutive heterochromatin and satellite DNA. De novo variations of constitutive heterochromatin may be useful as markers of exposure to mutagens and/or carcinogens.

Search for DNA interchange corresponding to sister chromatid exchanges in Chinese hamster ovary cells

Chinese hamster ovary cells (CHO) grown for one cycle in bromodeoxyuridine (BrdU) contain a small amount (0.5%) of unusually dense double stranded DNA. This dense DNA has been previously interpreted as being bifilarly substituted with BrdU and hence evidence that sister chromatid exchange (SCE) formation proceeds via the Holliday model of recombination. However, the amount of this dense DNA is 100 times greater than that expected based on the SCE frequency in similarly cultured CHO cells, and it is not increased by treating the cells with mitomycin C. Moreover, contrary to expectations for bifilary substituted DNA, the amount of this dense DNA is not reduced by growing BrdU-labeled cells for a second cycle in TdR. Finally, DNA isolated from CHO cells contains a minor band (0.5%) with a density 0.025 gm/cc greater than that of the main band, whether or not BrdU has been incorporated. These results call into question the identification of this unusually dense DNA as bifilarly substituted and hence its previously postulated relationship to SCE formation.

Postreplication repair in mammalian cells after ultraviolet irradiation: a model

A model is presented for bypass of ultraviolet-induced damage in DNA during replication. The overall process is initiated by the introduction of a single-strand break into parental DNA near the point of arrest of synthesis, followed by a transient crossing-over step similar to that envisaged in genetic recombination. The mechanism proposed provides an alternative explanation to existing models and is entirely consistent with available data on postreplication repair in mammalian cells. In addition the model explains the low level of recombination repair observed in mammalian cells.

Replication bypass model of sister chromatid exchanges and implications for Bloom's syndrome and Fanconi's anemia

A model of the sister chromatid exchange (SCE) process is outlined as a replication mechanism to bypass DNA crosslinks. The model suggests that when normal bidirectional replication advances from both sides towards a crosslink along the two opposite parental strands, the complementary parental strand segments can be temporarily displaced at each contralateral 5' side from the crosslink. The free ends produced in this first step will be terminally aligned but will have opposite polarity. The second step of the bypass can, however, be completed by either of two rejoining processes--terminal ligation of the free ends via nascent Okazaki pieces or aberrant complementation by overlapping the free ends. This bypass mechanism (1) allows replication to continue past a crosslink leaving it intact but (2) results in the switching of parental strands and their attached incomplete nascent strands above and below the crosslink site producing an exchange between sister chromatids. This model is compatible with the findings of current SCE studies using the new BUDR/stain techniques as well as with previous autoradiographic studies. It also suggests that the chromatid breaks and deletions in Fanconi's Anemia represent a defect in step two of the replication bypass mechanism and that the high frequency of SCE's and quadriradials in Bloom's Syndrome represent the SCE overload effects of a defect in crosslink repair.

Biochemical analysis of genetic recombination in eukaryotes

Recent studies concerning molecular mechanisms of genetic recombination in eukaryotes are reviewed. Since many of these studies have focused on the testable predictions arising from the hybrid DNA theory of genetic recombination, this theory is summarised. Experiments to determine the time of meiotic crossing-over and the structure of the synaptonemal complex which facilitates meiotic crossing-over are described. Investigations of DNA nicking and repair events implicated in recombination are discussed. Properties of proteins which may facilitate hybrid DNA formation, and biochemical evidence for hybrid DNA formation are presented. Finally, a nuclease which has been implicated in gene conversion is described.

Low-level DNA exchanges in normal human and xeroderma pigmentosum cells after UV irradiation

We have used a T4 endonuclease V assay method for UV-induced pryrimidine dimers in cellular DNA in vivo to obtain evidence for recombinational DNA exhanges after UV irradiation of normal human and Xeroderma pigmentosum (XP) cells. Our data indicate that the endonuclease-sensitive sites in excision-defective XP cells are removed very slowly from the irradiated parental strands and appear concomitantly in daughter strands newly synthesized during post-UV incubation. In the defective XP cells, the extent of appearance of sensitive sites in daughter strands synthesized during a period of 24 h after 10 J/m2 appears to be small, probably less than 15% of the initial number of sensitive sites detected in cellular parental strands. Demonstration of such exchanges between normal-density parental and 5-bromodeoxyuridine-labeled daughter strands by alkaline CsCl isopycnic centrifugation was unsuccessful. Further, the extent is much lower in normal human cells because of their efficient excision repair of the dimers before and after exchanges than in the defective XP cells.

Characterization of foldback sequences in hamster DNA using electron microsocpy

Foldback sequences in nuclear DNA from cultured Hamster fibroblasts (BHK-21/C13 cells) have been characterized by electron microscopy. One half of the structures observed when denatured hamster DNA is allowed to anneal in the range O less than Cot1 less than 1 x 10(-4) M sec result from the annealing of inverted sequences forming foldback DNA. The remainder have a probable bimolecular origin. arising from rapidly-annealing sequences of satellite-like complexity. The average length of the inverted sequences in the foldback molecules is about 0.9 kilobases. There is estimated to be about 42,000 such sequences (21,000 pairs) in the hamster genome, approximately 45% of which form looped structures with a mean loop length of 1.74 kilobases. Contrary to previous reports, binding of the renatured duplex molecules to hydroxyapatite results in a poor recovery of structures containing identifiable foldback sequences, due to preferential enrichment of the bound fraction with duplexes formed by intermolecular annealing.

Evidence for the formation of hybrid DNA during mitotic recombination in Chinese hamster cells

Direct evidence is provided for the formation of hybrid DNA during mitotic recombination in CHO cells. The cells were labeled for one round of replication in medium containing BUdR, so that the density of the DNA was heavy light (HL) and then returned to light medium. Further DNA synthesis, during either repair or chromosome replication, can only result in HL or fully light (LL) DNA; however, the formation of hybrid DNA as part of the process of recombinational repair will produce some fully heavy (HH) DNA. A small fraction of DNA containing regions of HH DNA has been detected on neutral CsC1 gradients, and the amount of this DNA is increased by treatment of the cells with mitomycin C. Increasing doses of mitomycin C produce smimlar increases in both the amount of HH DNA and the frequency of sister chromatid exchanges measured cytologically. This correlation provides evidence that the HH DNA is hybrid DNA, formed as an intermediate in recombinational repair.

A study of foldback DNA

Nuclear DNA from eucaryotes contains a significant fraction which forms duplexes very rapidly and also independently of the DNA concentration. This fraction can be isolated by adsorption to hydroxylapatite and has been called foldback DNA (Britten and Smith, 1970). Here we extend previous studies to show that the foldback fraction is due to the existence of a finite number of foldback foci in each genome equivalent of DNA, approximately 10(5) in the case of Xenopus laevis. More significantly, we have isolated the foldback fraction in quantity from DNA of such a size (in one case broken randomly and in another digested with a restriction endonuclease) that only about 10% of the total DNA has foldback properties. If the foldback foci were located in precisely the same positions in all sets of the Xenopus laevis genome, the prediction would be that these foldback fractions would contain sequences representing 20% (random shear) and 10% (restriction endonuclease) of the total genome. In contrast, our results show that in both cases the foldback fraction contains the entire Xenopus laevis DNA sequence. One possible explanation of these observations is that as in procaryotes, eucaryotic DNA is randomly cross-linked. We show that cross-linkage of Xenopus laevis DNA is not sufficient to explain our observations. In consequence, we have adopted the hypothesis that the formation of foldback DNA is mainly an intrastrand phenomenon, but nevertheless occurs at different sites in different sets of the Xenopus laevis genome.