Effect of insertions, deletions, and double-strand breaks on homologous recombination in mouse L cells

TAL effectors: tools for DNA targeting

Xanthomonas phytopathogenic bacteria produce unique transcription activator-like effector (TALE) proteins that recognize and activate specific plant promoters through a set of tandem repeats. A unique TALE-DNA-binding code uses two polymorphic amino acids in each repeat to mediate recognition of specific nucleotides. The order of repeats determines effector’s specificity toward the cognate nucleotide sequence of the sense DNA strand. Artificially designed TALE-DNA-binding domains fused to nuclease or activation and repressor domains provide an outstanding toolbox for targeted gene editing and gene regulation in research, biotechnology and gene therapy. Gene editing with custom-designed TALE nucleases (TALENs) extends the repertoire of targeted genome modifications across a broad spectrum of organisms ranging from plants and insect to mammals.

Processed pseudogenes are located preferentially in regions of low recombination rates in the human genome

The aim of this article is to demonstrate possible recombination-associated evolutionary forces affecting the genomic distribution of processed pseudogenes. The relationship between recombination rate and the distribution of processed pseudogenes is analysed in the human genome. The results show that processed pseudogenes preferentially accumulate in regions of low recombination rates and this correlation cannot be explained by indirect relationships with GC content and gene density. Several explanatory models for the observation are discussed. A model of selection against ectopic recombination is tested based on the difference in distribution pattern between two classes of processed pseudogenes, which differ in the possibility of stimulating ectopic recombination. Our results indicate that the correlation between processed pseudogene density and recombination rate is probably results, in part, from the selection against ectopic recombination between closely located homologous processed pseudogenes. We also found a length effect in processed pseudogene distribution, namely long processed pseudogenes are located more preferentially in regions of low recombination rates than short ones.

Homologous recombination-mediated double-strand break repair in mouse testicular extracts and comparison with different germ cell stages

Homologous recombination (HR) is established as a significant contributor to double-strand break (DSB) repair in mammalian somatic cells; however, its role in mammalian germ cells has not been characterized, although being conservative in nature it is anticipated to be the major pathway in germ cells. The germ cell system has inherent limitations by which intact cell approaches are not feasible. The present study, therefore, investigates HR-mediated DSB repair in mouse germ cell extracts by using an in vitro plasmid recombination assay based on functional rescue of a neomycin (neo) gene. A significantly high-fold increase in neo+ (Kan(R)) colonies following incubation of two plasmid substrates (neo delta1 and neo delta2) with testicular extracts demonstrated the extracts' ability to catalyze intermolecular recombination. A significant enhancement in recombinants upon linearization of one of the plasmids suggested the existence of an HR-mediated DSB repair activity. Comparison of the activity at sequential developmental stages, spermatogonia, spermatocytes and spermatids revealed its presence at all the stages; spermatocyte being the most proficient stage. Further, restriction analysis of recombinant plasmids indicated the predominance of gene conversion in enriched spermatocytes (mostly pachytenes), in contrast to gonial and spermatid extracts that showed higher reciprocal exchange. In conclusion, this study demonstrates HR repair activity at all stages of male germ cells, suggesting an important role of HR-mediated DSB repair during mammalian spermatogenesis. Further, the observed preference of gene conversion over reciprocal exchange at spermatocyte stage correlates with the close association of gene conversion with the meiotic recombination program.

Attempted base excision repair of ionizing radiation damage in human lymphoblastoid cells produces lethal and mutagenic double strand breaks

A significant proportion of cellular DNA damages induced by ionizing radiation are produced in clusters, also called multiply damaged sites. It has been demonstrated by in vitro studies and in bacteria that clustered damage sites can be converted to lethal double strand breaks by oxidative DNA glycosylases during attempted base excision repair. To determine whether DNA glycosylases could produce double strand breaks at radiation-induced clustered damages in human cells, stably transformed human lymphoblastoid TK6 cells that inducibly overexpress the oxidative DNA glycosylases/AP lyases, hNTH1 and hOGG1, were assessed for their radiation responses, including survival, mutation induction and the enzymatic production of double strand breaks post-irradiation. We found that additional double strand breaks were generated during post-irradiation incubation in uninduced TK6 control cells. Moreover, overproduction of either DNA glycosylase resulted in significantly increased double strand break formation, which correlated with an elevated sensitivity to the cytotoxic and mutagenic effects of ionizing radiation. These data show that attempted repair of radiation damage, presumably at clustered damage sites, by the oxidative DNA glycosylases can lead to the formation of potentially lethal and mutagenic double strand breaks in human cells.

Pseudogenes: are they "junk" or functional DNA?

Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes.

Analysis of recombination sites within the maize waxy locus

Genetic fine structure analysis of the maize wx locus has determined that the ratio of genetic to physical distance within wx was one to two orders of magnitude higher than the average for the maize genome. Similar results have been found at other maize loci. In this study, we examined several mechanisms that could account for this pattern. First, crossovers in two other maize genes resolve preferentially at specific sites. By mapping exchanges between wx-B1 and wx-I relative to a polymorphic SstI site, we found no evidence for such a hotspot at wx. Second, deletion of promoter sequences from wx alleles had little effect on recombination frequencies, in contrast to results in yeast where promoter sequences are important for initiating recombination in some genes. Third, high levels of insertion polymorphism may suppress intergenic recombination. However, the presence of a 2-kb Ds element 470 bp upstream of the wx transcription start site did not further suppress recombination between Ds insertions in nearby wx sequences. Thus, none of these mechanisms is sufficient to explain the difference between intergenic and intragenic recombination rates at wx.

Two types of double-strand breaks in electron and photon tracks and their relation to exchange-type chromosome aberrations

Yields of DNA double-strand breaks (dsb), i.e. the average number of dsb, N, per relative molar mass, M(r), and dose, D, produced by electrons and photons in the energy range 50 eV-1 MeV were calculated. The experimental data of dsb induction by ultrasoft x-rays and by photons agree well with the calculated yields of dsb as a function of photon energy. The dsb are classified into simple and complex ones. Energy transfers of less than about 200 eV producing at least two ionizations generate mainly simple dsb, while low-energy electrons with an initial energy between 200 and 500 eV induce preferentially complex dsb. Assuming that dsb is the main DNA lesion leading to exchange-type chromosome aberrations (etca), three different mechanisms have to be considered: 1) complex dsb on its own; 2) interaction between two dsb induced by the same primary particle; and 3) interaction between two dsb induced by different primary particles. Mechanisms 1) and 2) produce a linear term, whereas mechanism 3) leads to a quadratic term for the yield of etca. The sum of contributions 1) and 2) to the yield of dicentrics describes fairly well the non-trivial structure of the experimental data. The results suggest that interaction between complex dsb does not contribute significantly to the formation of dicentrics via mechanism 3).

Effects of DNA topoisomerase inhibitors on nonhomologous and homologous recombination in mammalian cells

To study the involvement of DNA topoisomerases in recombination in mammalian cells, we used gene transfer assays to examine the effects of DNA topoisomerase inhibitors on nonhomologous (illegitimate) and homologous recombination. The assays were performed by transfecting adenine phosphoribosyltransferase-deficient (APRT-) CHO cells with plasmids carrying the wild-type or mutant aprt genes and by treating the cells with the inhibitors, followed by subsequent cultivation to select for APRT-positive (APRT+) colonies. Treatments with DNA topoisomerase II inhibitors such as VP-16, VM-26, ICRF-193 resulted in a 3- to 5-fold stimulation of integration of both closed-circular and linearized plasmids carrying the wild-type aprt gene into the recipient genome through nonhomologous recombination. The same treatments also increased 6- to 9-fold and 3-fold the number of APRT+ recombinant colonies that were generated by cotransfecting two closed-circular plasmids with nonoverlapping defective aprt genes and their linearized equivalents, respectively. However, this cotransfection assay involved intrinsically nonhomologous recombination processes; normalization of the frequencies by dividing them with those of the above nonhomologous recombination revealed 2-fold enhancement of homologous recombination events between the circular mutant genes but not between the linear ones. In contrast, DNA topoisomerase I inhibitor, camptothecin, showed no such effect on either recombination. From these results, we discuss the function of DNA topoisomerases on recombination in mammalian cells.

Primary products of break-induced recombination by Escherichia coli RecE pathway

Alternative models for break-induced recombination predict different distributions of primary products. The double-stranded break-repair model predicts a noncrossover product and equimolar amounts of two crossover products. The one-end pairing model predicts two crossover products, but not necessarily in equimolar amounts, and the single-stranded annealing model predicts deletion of the fragment between the pairing sequences. Depending on the structure of the recombining substrate(s) and the nature of the resectioning step that precedes strand annealing, the single-stranded annealing mechanism would yield only one or both crossover products. We tested these predictions for the RecE recombination pathway of Escherichia coli. Nonreplicating intramolecular recombination substrates with a double-stranded break (DSB) within one copy of a direct repeat were released from chimera lambda phage by in vivo restriction, and the distribution of primary circular recombination products was determined. Noncrossover products were barely detectable, and the molar ratio of the two crossover products was proportional to the length ratio of the homologous ends flanking the DSB. These results suggest an independent pairing of each end with the intact homolog and argue against the double-stranded break-repair model. However, the results do not distinguish alternative pairing mechanisms (strand invasion and strand annealing). The kinetics of heteroduplex formation and heteroduplex strand polarity were investigated. Immediately following the DSB induction, heteroduplex formation was done by pairing the strands ending 3' at the break. A slow accumulation of the complementary heteroduplex made by the pairing of the strands ending 5' at the break (5' heteroduplexes) was observed at a larger stage. The observed bias in heteroduplex strand polarity depended on DSB induction at a specific site. The 5' heteroduplexes may have been generated by reciprocal strand exchange, pairing that is not strand specific, or strand-specific pairing induced at random breaks.

Unstable integration of transfected DNAs into embryonal carcinoma cells

Plasmid DNA can be efficiently transfected into embryonal carcinoma cells but it is difficult to isolate clones of cells stably expressing genes present on the transfected plasmids. Even in clonal populations derived from transfected cells, the introduced genes are expressed in some but not all cells. Cotransfection with a region of the Pgk-1 gene results in more efficient, stable cotransformation due to increased numbers of copies of the transfected plasmids integrated into the genomic DNA. The PgK-1 genomic sequences did not allow the plasmid DNA to replicate autonomously but seemed to enhance the ligation of transfected plasmids before their integration into the host genome. Our results suggest a model in which the plasmid DNAs are able to integrate and subsequently excise from the host genome by recombination events enhanced by transcription through the tandemly repeated sequences of the transfected plasmids.

Targeting vector configuration and method of gene transfer influence targeted correction of the APRT gene in Chinese hamster ovary cells

A 21-bp deletion in the third exon of the APRT gene in Chinese hamster ovary (CHO) cells was corrected by transfection with a plasmid containing hamster APRT sequences. Targeted correction frequencies in the range of 0.3-3.0 x 10(-6) were obtained with a vector containing 3.2 kb of APRT sequence homology. To examine the influence of vector configuration on targeted gene correction, a double-strand break was introduced at one of two positions in the vector prior to transfection by calcium phosphate-DNA coprecipitation or electroporation. A double-strand break in the region of APRT homology contained in the vector produced an insertion-type vector, while placement of the break just outside the region of homology produced a replacement-type vector. Gene targeting with both linear vector configurations yielded equivalent ratios of targeted recombinants to nontargeted vector integrants; however, targeting with the two different vector configurations resulted in different distributions of targeted recombination products. Analysis of 66 independent APRT+ recombinant clones by Southern hybridization showed that targeting with the vector in a replacement-type configuration yielded fewer targeted integrants and more target gene convertants than did the integration vector configuration. Targeted recombination was about fivefold more efficient with electroporation than with calcium phosphate-DNA coprecipitation; however, both gene transfer methods produced similar distributions of targeted recombinants, which depended only on targeting vector configuration. Our results demonstrate that insertion-type and replacement-type gene targeting vectors produce similar overall targeting frequencies in gene correction experiments, but that vector configuration can significantly influence the yield of particular recombinant types.

Reconstitution of an episomal mouse aprt gene as a consequence of recombination

When a functional murine adenine phosphoribosyltransferase (aprt) gene linked to bovine papilloma virus (BPV) DNA is transfected into Aprt- L cells, the cells are rendered Aprt+ and the aprt gene persists as an episome. Cotransfection with two BPV vectors, one containing the 5' half of the aprt gene and the other the 3' half of the gene, that share about 300 bp of common sequence in intron 2, produces Aprt+ cells with functional aprt as an episome. Southern blot analysis of low molecular weight DNA derived from Hirt extracts revealed the regeneration of a diagnostic SmaI fragment, consistent with establishment of an episome with functional aprt that was reconstituted as a consequence of recombination. To establish cells with an episomal target for recombination, BPV vectors containing a G418 resistance marker and either the 5' half or 3' half of aprt were transfected into Aprt- L cells. Stably transfected cells, selected by their growth in G418, were in turn transfected with DNA containing the other half of the aprt gene. Following selection of Aprt+ cells, Southern blot and polymerase chain reaction (PCR) analysis of low molecular weight DNA confirmed the presence of a complete episomal aprt gene. The region of DNA shared by the episomal aprt fragment and the transfected aprt half was sequenced after PCR amplification of the reconstituted, episomal gene and was found to be wild type. The region of overlap that serves as the substrate for recombination lies entirely within an intron and can, therefore, tolerate nucleotide substitutions and deletions. The absence of such errors in the sequences examined is consistent with recombination events that are not error prone.

The mechanism of extrachromosomal homologous DNA recombination in plant cells

By cotransfecting plasmids carrying particular mutations in the beta-glucuronidase (GUS) gene into Nicotiana plumbaginifolia protoplasts and by monitoring the recombination rates using a recently developed transient assay, we were able to obtain insights into the mechanism of extrachromosomal recombination operating in plant cells. An exchange of flanking markers takes place in over 90% of the recombination events. In most of the remaining cases two consecutive, independent single crossover events occur. These events involve the same DNA substrate and lead to two successive exchanges of flanking markers, thus mimicking a presumed double crossover intermediate. A comparison of the outcome of our experiments with the predictions of two recombination models originally proposed for mammalian cells indicates that extrachromosomal recombination in plant cells is best described by the single strand annealing model. According to this model all recombination events result in an exchange of flanking markers. Our results rule out the double strand break repair model which predicts that flanking markers are exchanged in only half of all events.

Repetitive sequences involved in the recombination leading to deletion of exon 5 of the low-density-lipoprotein receptor gene in a patient with familial hypercholesterolemia

Alu sequences in the low-density-lipoprotein (LDL) receptor gene are suspected of being of importance for the creation of gene defects leading to familial hypercholesterolemia (FH). One potential mechanism is that Alu sequences undergo homologous recombination, producing deletions or duplications of DNA segments on genomic DNA. In at least four cases (FH626, PO, JA and FH-DK3), a deletion of exon 5 of the LDL receptor gene has been reported. Only one of these (FH626) have so far been characterized in detail by sequence analysis and shown to involve two of the Alu repeated sequences, which are present in introns 4 and 5. We here report the complete characterization of FH-DK3 and show that the cross-over break points involve sequences similar, but not at identical positions in the 5' end, to those reported for FH626. The recombinations in both FH-DK3 and FH626 are suggested to have occurred within a 22-bp repeated sequence found in both junction alleles.

Intrachromosomal recombination in plants

Molecular evidence for intrachromosomal recombination between closely linked DNA repeats within the plant genome is presented. The non-overlapping complementary deletion derivatives of the selectable neomycin phosphotransferase gene (nptII), when intact conferring kanamycin resistance, were inserted into the genome of Nicotiana tabacum. The functional marker gene was restored with frequencies between 10(-4) and 10(-6) per proliferating cell clone. Prolonged tissue culture prior to kanamycin selection did not increase the number of recombinant kanamycin-resistant (KanR) cell clones. DNA analysis of KanR clones derived from cells carrying multiple tandem recombination units suggested that these units have a tendency to undergo concerted recombination. Recovery and analysis of kanamycin-sensitive seedlings with patches of KanR cells provided direct evidence for mitotic recombination in plant tissue.

Homologous recombination is elevated in some Werner-like syndromes but not during normal in vitro or in vivo senescence of mammalian cells

Werner syndrome (WS) is a recessive genetic condition associated with markedly reduced replicative lifespans of cells in culture, high chromosomal instability in vivo and in vitro, and premature appearance of many characteristics of normal aging, including an increased incidence of cancer. We have monitored plasmid homologous recombination frequencies in diploid fibroblasts from 6 Werner or Werner-like syndrome patients, following transfection with a plasmid substrate containing 2 overlapping fragments of the TN5 Neor gene. Plasmid DNA recovered from these cells was then assayed for homologous recombination by (a) transformation of recA- bacteria to Ampr (indicating total viable plasmid) or Neor (indicating viable recombinant plasmid), and (b) by limited-cycle polymerase chain reaction (PCR) to co-amplify a recombinant fragment containing the overlap region, and a control region of the same plasmid, without bacterial transformation. Bacterial assay data indicated that recombination rates in 3 of the 6 WS strains were significantly elevated above normal controls; 4 of 6 appeared elevated by PCR assay. The highest-recombination WS strain showed evidence of reduced degradation of transfected plasmid DNA. For this small sample of WS strains, clinical severity of WS was not well correlated with recombination rate as determined by either assay (Pearson r = 0.78, not significant, for PCR assay); elevated recombination may, however, define a subset of WS at greatest risk for cancer and/or atherosclerosis. PCR assay of a hyperoxia-resistant HeLa cell line, displaying substantially increased chromosome breakage, indicated increased recombination between direct-repeat fragments. Nevertheless, elevated recombination in WS strains is unlikely to be secondary to impaired replicative capacity characteristic of WS cells, or to defective repair of chromosome damage which is increased in WS, since recombination in non-WS strains was unaffected by passage level or repeated UV irradiation.

Relative frequencies of homologous recombination between plasmids introduced into DNA repair-deficient and other mammalian somatic cell lines

Twelve mammalian somatic cell lines, some of them DNA damage-sensitive mutants paired with their respective wild-type parental lines, were assayed for their ability to catalyze extrachromosomal, intermolecular homologous recombination between pSV2neo plasmid recombination substrates. All of the somatic cell lines analyzed are capable of catalyzing homologous recombination; however, there is a wide range of efficiencies with which they do so. Five human cell lines display a fourfold range of recombination frequencies, and six hamster cell lines vary almost 20-fold. Linearizing one of the recombination substrates stimulates recombination in all but one of the cell lines. Two of the three paired mutant cell lines display a threefold reduction in their ability to catalyze homologous recombination when compared to their respective parental cell lines, indicating that the mutations that render them sensitive to DNA damaging agents might also play a role in homologous recombination.

Targeted gene modification for gene therapy of stem cells

Ideally, gene therapy would correct the specific gene defect without adding potentially harmful extraneous DNA sequences. Such correction can be obtained with homologous recombination between input DNA sequences and identical (homologous) sequences in the genomic target gene. The development of techniques for obtaining virtually pure populations of hematopoietic stem cells should permit the use of the highly efficient nuclear microinjection methods for transfer of DNA. These techniques combined with new highly sensitive methods for detecting cells with the specified genetic modification of nonexpressed genes would make homologous recombination-mediated gene therapy feasible for hematopoietic stem cells. These advances are reviewed with particular emphasis on approaches to targeted gene modification of hematopoietic stem cells and speculation on directions for future research.

Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells

Hypervariable minisatellite DNA sequences are short tandemly repeated sequences that are present throughout the human genome and are implicated to enhance recombination. We have constructed a consensus hypervariable minisatellite sequence and analyzed its effect on homologous recombination in human cells in culture. The consensus sequence d(AGAGGTGGGCAGGTGG)6.5 is shown to stimulate homologous recombination up to 13.5-fold. The stimulation occurs at a distance and in both directions but does show a quantitative directionality. Stimulation occurs in a codominant manner, and the sequence is inherited equally in the products. Enhancement is maintained, but at a reduced level, when double-strand breaks are introduced into the substrates. Multiple unselected recombination events are promoted, and preferential stimulation of reciprocal exchange events is demonstrated.

Use of damaged plasmid to study DNA repair in X-ray sensitive (xrs) strains of Chinese hamster ovary (CHO) cells

The effect of gamma-irradiation of pSV2gpt DNA on its transfection frequency has been analysed using CHO xrs mutants. Xrs mutants are sensitive to ionizing radiation and show a defect in double-strand break (dsb) rejoining. At low doses a sharp decrease in relative transfection frequency, i.e. transfection frequency of irradiated plasmid relative to untreated plasmid, was observed in the xrs mutants compared with the parent line K1. Electrophoresis of the irradiated plasmid DNA showed that the decrease in transfection frequency in the xrs mutants correlated with the change of supercoiled molecules into open-circular forms. One explanation for these results is that the xrs gene could play a part in the integration or repair of open-circular molecules produced by gamma-radiation. In the parent line CHO-K1, open-circular and supercoiled molecules have the same transfection frequency. The effect of linearization of pSV2gpt DNA by restriction enzymes on transfection frequency in xrs and wild-type strains has also been examined. In contrast to the above results we have not detected a difference in the relative transfection frequency between xrs and wild-type strains. The results suggest that restricted plasmid DNA is subject to extensive nucleolytic degradation, and this occurs to equal extents in wild type and mutant strains.

A genetic investigation of the mechanism of adenovirus marker rescue

We have developed quantitative and segregational methods for investigating the mechanism of genetic exchange in adenovirus marker rescue. Estimates of "marker rescue frequency" (m.r.f.) were used to show that marker rescue increases linearly with increasing dose of fragment up to equimolarity with the full-length genome. The m.r.f. is also affected by the size of the rescuing fragment and the position of the wild-type allele within it, regardless of whether the fragment is terminal or internal. This is compatible with marker rescue being based on homologous exchange between the recombining partners. Examination of individually transfected cells showed that there is very wide variability in the values of the m.r.f.'s. This suggests that marker transfer can occur after replication of the full-length genome has begun, and can occur late into the infectious cycle. Unselected markers on the rescuing fragment were shown to be co-inherited frequently. This suggests that physical linkage is accompanied by genetic linkage. To examine this more closely, a multifactorial marker rescue was performed. The data show unequivocally that markers resident on the same fragment as the selected allele are inherited at high frequency, with a gradient of transfer in which markers closest to the selected marker are transferred most frequently. Markers up to 13 and perhaps as many as 17 kb apart can be inherited together. There are very few examples of the inheritance of distal markers in the absence of proximal ones. These data suggest that large pieces of DNA are transferred in a concerted reaction during marker rescue.

Decreased stable transfection frequencies of six X-ray-sensitive CHO strains, all members of the xrs complementation group

Six X-ray-sensitive strains (xrs) of the Chinese hamster ovary (CHO) cell line, all of which have a defect in double-strand break (dsb) rejoining, have been investigated for their proficiency in DNA transfection assays. All 6 strains and clonal isolates derived from them, show a decreased stable transfection frequency using the plasmids pSV2neo and pSV2gpt after transfection by either the CaPh method or the polybrene method. The magnitude of this effect is DNA concentration dependent and is more marked after transfection with higher DNA concentrations (5-20 micrograms DNA). A spontaneous X-ray-resistant reactivant (or revertant) of one xrs strain also acquired the elevated transfection frequency of the wild-type strain providing evidence for a causal relationship between the decreased transfection frequency and the xrs phenotype. In contrast, the strains show no defect when transfection is assayed using a transient transfection system. Since the transient transfection assay only depends on the uptake and transcriptional activity of foreign DNA, and does not necessitate DNA integration, this suggests that the xrs strains do not have a defect in the uptake of foreign DNA, but might have a defect in integration or the processing of DNA molecules prior to integration.

Analysis of recombination in mammalian cells using SV40 and SV40-derived vectors

Viruses and viral vectors have played a crucial role in our understanding of the pathways of homologous and non-homologous recombination in mitotically dividing mammalian cells. In particular, they have allowed the confirmation of the preponderance of non-homologous over homologous recombination events and led to schemes for the selection and isolation of homologous recombination products. These studies have allowed an examination of the properties of reciprocal and non-reciprocal homologous recombination events extrachromosomally, in the chromosome and between plasmids and chromosomes. They suggest that it is feasible now to direct DNA segments to predetermined chromosomal locations by homologous recombination.

Molecular analysis of homologous recombination catalysed by human nuclear extract: fidelity and DNase protection

We present a molecular analysis of DNA's resulting from homologous recombination, between two duplex molecules, and catalysed by human nuclear extracts. Sequence analysis of 20 recombined clones (400 nucleotides per clone), in a genetically silent sequence surrounding the recombination initiation or termination site, shows no modification compared to the parental sequence. Transient protection of the DNA's against DNase treatment was brought about by the nuclear extract. This protection was found to be strickly confined to the homologous sequences potentially implicated in recombination.

Effect of gamma rays on efficiency of gene transfer in DNA repair-proficient and -deficient cell lines

Ionizing radiation induces a number of molecular changes in cells, including DNA damage, mutation, genetic recombination, gene amplification, and chromosomal rearrangement. The studies described here make use of the process of DNA-mediated gene transfer to examine the molecular effects of ionizing radiation. Two Chinese hamster ovary cell lines, the wild-type, AA8-4, and a DNA repair-deficient line, EM9-1, that is sensitive to ionizing radiation, were transfected with the recombinant DNA plasmid, pSV2-GPT, either in the absence or presence of high-molecular-weight carrier DNA. Following transfection, cell populations were irradiated with graded doses of 137Cs gamma-rays. Results demonstrate that, on a per viable cell basis, ionizing radiation hinders the transfection of this plasmid when tested in the presence of carrier DNA. A similar dose response was seen for both the wild-type (AA8-4) and mutant (EM9-1) lines. However, in the absence of carrier DNA, 137Cs gamma-rays clearly enhanced the gene transfer process. An enhancement factor of 3-5 was seen for AA8-4 cells and 2-3 for EM9-1 cells. This enhancement occurred at relatively low doses (e.g., 50 cGy) and was not substantially elevated by larger doses.

Correction of deletions in mammalian cells by gene conversion

We have constructed substrates to study the conversion of deletions in mammalian cells both extrachromosomally and after the stable integration of the substrates into the chromosome. These substrates were designed to study gene conversion without the complication of reciprocal recombination events. The substrates contain insertion or deletion mutations of the neomycin resistance gene (neo) and an internal, homologous fragment of the neo gene (neo-526), such that gene conversion from neo-526 to the mutated neo gene restores a functional neo gene. We have shown that extrachromosomally insertions of 10 bp or deletions of 22 or 167 bp are converted to wild-type at similar frequencies (1-6 X 10(-4)). Chromosomal gene conversion occurred at frequencies of about 10(-6)-10(-7) per cell generation. As expected from the experimental design, all recombination events analyzed in mammalian cells using these substrates appear to be due to gene conversion.

Homologous recombination in a Chinese hamster X-ray-sensitive mutant

We have tested the mutant Chinese hamster cell line xrs-5, which is sensitive to ionizing radiation, for the ability to carry out homologous recombination. In an in vivo assay to detect recombination between two transfected plasmids carrying non-complementing mutants in the neomycin resistance gene, xrs-5 showed a 6-fold reduction in recombination frequency when compared to the parental cell line K1. Extracts prepared from nuclei of the mutant were also tested for their ability to catalyze homologous recombination between the same two plasmids in vitro. Extracts from xrs-5 were found to mediate recombination in this assay at frequencies not significantly different from those obtained with extracts from the parental cell line.

Analysis of homologous recombination in cultured mammalian cells in transient expression and stable transformation assays

Recombination between plasmid molecules, each containing a nonoverlapping deletion mutation in the hamster adenine phosphoribosyltransferase gene, was measured after coinjection into rat cells. Using these two plasmids, as linear or circular molecules, the recombination efficiency was measured soon after injection in a transient expression assay or after selection for stable transformants. The transient assay revealed that linear molecules were a better substrate for recombination, with double strand breaks within the region of homology stimulating recombination more than breaks outside the region of homology. A 20 to 70-fold increase in the efficiency of recombination was observed when two linear molecules were coinjected as compared to two circular molecules. Linear molecules were found to not only stimulate recombination but also to facilitate stable integration of the recombinant molecule into the host genome.