Analysis of restriction enzyme-induced chromosomal aberrations by fluorescence in situ hybridization

Exogenous enzymes upgrade transgenesis and genetic engineering of farm animals

Transgenic farm animals are attractive alternative mammalian models to rodents for the study of developmental, genetic, reproductive and disease-related biological questions, as well for the production of recombinant proteins, or the assessment of xenotransplants for human patients. Until recently, the ability to generate transgenic farm animals relied on methods of passive transgenesis. In recent years, significant improvements have been made to introduce and apply active techniques of transgenesis and genetic engineering in these species. These new approaches dramatically enhance the ease and speed with which livestock species can be genetically modified, and allow to performing precise genetic modifications. This paper provides a synopsis of enzyme-mediated genetic engineering in livestock species covering the early attempts employing naturally occurring DNA-modifying proteins to recent approaches working with tailored enzymatic systems.

Classical and molecular cytogenetics in analysis of diepoxybutane-induced chromosome aberrations

The genotoxic properties of diepoxybutane (DEB) have been extensively studied by many authors. The most often investigated endpoints were sister chromatid exchanges (SCE) and micronuclei (MN), and less frequently, chromosome aberrations (CAs). In the present study, the analysis of CAs induced by DEB in vitro on human whole blood lymphocytes was performed by using three methods of chromosome visualisation: Giemsa-staining, GTG banding and chromosome painting (FISH). The results showed that DEB is a very efficient clastogenic agent and induces chromosome breaks and gaps as well as tri- and quadriradials (observed by using classical cytogenetic methods) together with acentrics (observed by using FISH) on the statistically significant level, as compared to controls (chi2-test, p<10-5). The analysis of GTG-banded metaphases revealed that the break-points were distributed non-randomly within the chromosomes and located mainly in 1p, 1q, 2p, 2p, 6q, 9q and 14q (p<10-6). In conclusion it can be stated, that methods applied in this work are complementary and can be used successfully for estimation of the clastogenic potential of the tested chemical.

137Cesium-induced chromosome aberrations analyzed by fluorescence in situ hybridization: eight years follow up of the Goiânia radiation accident victims

The radiation accident in focus here occurred in a section of Goiânia (Brazil) where more than a hundred individuals were contaminated with 137Cesium on September 1987. In order to estimate the absorbed radiation doses, initial frequencies of dicentrics and rings were determined in 129 victims [A.T. Ramalho, PhD Thesis, Subsidios a tecnica de dosimetria citogenetica gerados a partir da analise de resultados obtidos com o acidente radiologico de Goiânia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil, 1992]. We have followed some of these victims cytogenetically over the years seeking for parameters that could be used as basis for retrospective radiation dosimetry. Our data on translocation frequencies obtained by fluorescence in situ hybridization (FISH) could be directly compared to the baseline frequencies of dicentrics available for those same victims. Our results provided valuable information on how precise these estimates are. The frequencies of translocations observed years after the radiation exposure were two to three times lower than the initial dicentrics frequencies, the differences being larger at higher doses (>1 Gy). The accuracy of such dose estimates might be increased by scoring sufficient amount of cells. However, factors such as the persistence of translocation carrying lymphocytes, translocation levels not proportional to chromosome size, and inter-individual variation reduce the precision of these estimates.

Chromosomal aberrations induced by defined DNA double-strand breaks: the origin of achromatic lesions

The mechanisms of formation of chromosomal aberrations are poorly understood, despite the common use of aberrations as a measure of the genetic effects of physical and chemical agents. We have used restriction endonucleases to introduce defined DNA double-strand breaks into mammalian cells, and measured chromosomal aberration formation relative to the activity of the endonuclease. The endonucleases AluI and Sau3AI remain active for a relatively short time under simulated cellular conditions and induce achromatic lesions ('gaps') in chromatids only within the first hour or two following treatment. In contrast, the endonuclease MboI (an isoschizomer of Sau3AI) is active for an extremely long time and continues to produce chromatid gaps during the whole 12 hr sampling period. This observation strongly suggests that the aberrations classified as gaps are a manifestation of unrejoined DNA double-strand breaks. The formation of gaps may relate to the opportunities for repair of DNA breaks in relation to cell-cycle position. It is more difficult to relate the formation of structural chromatid aberrations to the endonuclease activity, although at relatively low concentrations all 3 endonucleases gave similar levels of structural aberrations.

Human chromosome-specific changes in a human-hamster hybrid cell line (AL) assessed by fluorescent in situ hybridization (FISH)

PURPOSE

To quantitatively assess all gamma-ray induced chromosomal changes confined to one human chromosome using fluorescence microscopy and in situ hybridization with a fluorescently labeled human chromosome specific nucleic acid probe.

METHODS AND MATERIALS

Synchronized human-hamster hybrid cells containing human chromosome 11 were obtained by a modified mitotic shake-off procedure. G1 phase cells (> 95%) were irradiated with 137Cs gamma rays (0, 0.5, 1.0, 1.5, 2.0, 4.0, 6.0, 8.0, and 10.0 Gy) at a dose rate of 1.1 Gy/min and mitotic cells collected 16-20 h later; chromosomal spreads were prepared, denatured, and hybridized with a fluorescein-tagged nucleic acid probe against total human DNA. Chromosomes were examined by fluorescence microscopy and all categories of change involving the human chromosome 11 as target, recorded.

RESULTS

Overall, of the 3104 human-hamster hybrid cells examined, 82.1% were euploid, of which 88.6% contained one copy of human chromosome 11, 6.2% contained two copies, and 5.2% contained 0 copies. This is compatible with mitotic nondisjunction in a small fraction of cells. Of the remaining 17.9% of cells, 85.2% were tetraploid cells with two copies of human chromosome 11. For all aberrations involving human chromosome 11 there was a linear relationship between yield and absorbed dose of 0.1 aberrations per chromosome per Gy. The yield of dicentrics, translocations, and terminal deletions that involve one lesion on the human chromosome was linear, while the yield of interstitial deletions that arise from two interacting lesions on the human chromosome was curvilinear. The frequencies of dicentrics and translocations were about equal, while there was a high (40-60%) incidence of incomplete exchanges between human and hamster chromosomes.

CONCLUSIONS

Fluorescent in situ hybridization (FISH) procedures allow for the efficient detection of a broad range of induced changes in target chromosomes. Symmetrical exchanges induced in G1 (translocations) were readily scored and found to equate with the complementary asymmetrical exchanges (dicentrics). That is, nonlethal stable changes, which might be of concern in carcinogenic processes, complement lethal, unstable changes. Interstitial deletions that may contribute to the loss of antioncogenes as well as to lethality are also readily detected with enhanced levels detected at higher doses. The high level of induced terminal deletions and of incomplete dicentrics and translocations indicate a partial failure of interaction between lesions induced in human and hamster DNA, and suggest that such interspecies interactions lack the fidelity of intraspecies DNA lesion interactions. This suggests caution in the use of such model systems as indicators of human cell responsiveness.

DNA topoisomerase and recombinase activities in Nae I restriction endonuclease

Nae I endonuclease must bind to two DNA sequences for cleavage. Examination of the amino acid sequence of Nae I uncovered similarity to the active site of human DNA ligase I, except for leucine 43 in Nae I instead of the lysine essential for ligase activity. Changing leucine 43 to lysine 43 (L43K) changed Nae I activity: Nae I-L43K relaxed supercoiled DNA to yield DNA topoisomers and recombined DNA to give dimeric molecules. Interruption of the reactions of Nae I and Nae I-L43K with DNA demonstrated transient protein-DNA covalent complexes. These findings imply coupled endonuclease and ligase domains and link Nae I endonuclease to the topoisomerase and recombinase protein families.

Validation of chromosome painting. II. A detailed analysis of aberrations following high doses of ionizing radiation in vitro

Fluorescence in situ hybridization with chromosome-specific composite DNA probes ('chromosome painting') is useful for quantifying radiation-induced cytogenetic damage. Recently we showed that the frequency of aberrations observed with painting is similar to that seen with conventional cytogenetic methods, at least at doses of < or = 2 Gy. Above this dose, however, the agreement was not as good. We describe here the results of additional work designed to clarify our earlier findings, and provide a detailed analysis of the type and frequency of aberrations induced in human peripheral lymphocytes following acute exposure to 137Cs at doses of 0 (unexposed control), 1, 2, 3 and 4 Gy. The newly-developed nomenclature for chromosome aberrations detected by painting (Protocol for Aberration Identification and Nomenclature Terminology, 'PAINT') was used to classify all aberrations. Our results indicate that if the guidelines of the PAINT system are followed, chromosome painting can provide meaningful biodosimetry at high doses, and that the observation of complicated rearrangements not only does not interfere with dose estimation, but also the information provided by these exchanges can be easily broken down into the component aberrations and included in the dose estimate. We also show that the inequality between translocations and dicentrics that we previously observed can be explained by an excess of one class of translocated chromosomes, specifically those in which the centromere is from an unpainted chromosome. Translocated chromosomes in which the centromere is painted were found to occur at a frequency equal to dicentrics. These results should help clarify the use of painting for radiation biodosimetry by improving our understanding of the frequencies of various types of stable aberrations observed shortly after exposure. This will improve our ability to perform meaningful biodosimetry long after the frequencies of unstable aberrations have ceased to be informative.

Use of multicolour chromosome painting to identify chromosomal rearrangements in human lymphocytes exposed to bleomycin: a comparison with conventional cytogenetic analysis of Giemsa-stained chromosomes

Exchange aberrations induced by bleomycin were identified by multicolour fluorescence in situ hybridisation (FISH) with probes for chromosomes 1, 2, and 3. The frequency and distribution of aberration types were compared to conventional metaphase analysis of Giemsa-stained chromosomes from the same human lymphocyte cultures. The total percentage of exchanges detectable by painting three pairs of chromosomes with separate colours was calculated as 40%. Giemsa staining revealed predominantly asymmetric chromosome exchanges, which are expected to comprise 50% of the total induced exchanges. Genomic exchange frequencies were, therefore, determined by multiplying the observed frequencies from FISH analysis by 2.5 and the number of asymmetric exchanges identified in Giemsa-stained slides by 2.0. By these calculations, the genomic exchange frequency calculated from chromosome painting exceeded that estimated by Giemsa-staining. This difference was due to the identification by chromosome painting of a unique class of cells in which chromosomes had undergone complex exchanges (nonreciprocal exchanges involving multiple mutual sites). The percentage of cells exhibiting exchanges was similar for both methods.

Illegitimate recombination induced by DNA double-strand breaks in a mammalian chromosome

We examined DNA double-strand-break-induced mutations in the endogenous adenine phosphoribosyl-transferase (APRT) gene in cultured Chinese hamster ovary cells after exposure to restriction endonucleases. PvuII, EcoRV, and StuI, all of which produce blunt-end DNA double-strand breaks, were electroporated into CHO-AT3-2 cells hemizygous at the APRT locus. Colonies of viable cells containing mutations at APRT were expanded, and the mutations that occurred during break repair were analyzed at the DNA sequence level. Restriction enzyme-induced mutations consisted of small deletions of 1 to 36 bp, insertions, and combinations of insertions and deletions at the cleavage sites. Most of the small deletions involved overlaps of one to four complementary bases at the recombination junctions. Southern blot analysis revealed more complex mutations, suggesting translocation, inversion, or insertion of larger chromosomal fragments. These results indicate that blunt-end DNA double-strand breaks can induce illegitimate (nonhomologous) recombination in mammalian chromosomes and that they play an important role in mutagenesis.

Illegitimate recombination induced by DNA double-strand breaks in a mammalian chromosome

We examined DNA double-strand-break-induced mutations in the endogenous adenine phosphoribosyl-transferase (APRT) gene in cultured Chinese hamster ovary cells after exposure to restriction endonucleases. PvuII, EcoRV, and StuI, all of which produce blunt-end DNA double-strand breaks, were electroporated into CHO-AT3-2 cells hemizygous at the APRT locus. Colonies of viable cells containing mutations at APRT were expanded, and the mutations that occurred during break repair were analyzed at the DNA sequence level. Restriction enzyme-induced mutations consisted of small deletions of 1 to 36 bp, insertions, and combinations of insertions and deletions at the cleavage sites. Most of the small deletions involved overlaps of one to four complementary bases at the recombination junctions. Southern blot analysis revealed more complex mutations, suggesting translocation, inversion, or insertion of larger chromosomal fragments. These results indicate that blunt-end DNA double-strand breaks can induce illegitimate (nonhomologous) recombination in mammalian chromosomes and that they play an important role in mutagenesis.

Chromosome aberrations induced in vitro: mechanisms, delayed expression, and intriguing questions

Chromosome aberrations, including breakage and rearrangement and numerical changes, are important in carcinogenesis, heritable mutations, embryonic loss, and developmental abnormalities. We can detect DNA reactive agents in in-vitro chromosome aberrations assays, but aberrations are also induced by chemical that do not directly interact with DNA. This article discusses briefly some important aspects of using aberrations in genetic toxicology testing but concentrates on highlights of recent research on aberrations, in particular two areas: (1) persistence through multiple cell cycles of changes that lead to chromosome aberrations, and (2) the relations among DNA synthesis inhibition, DNA damage, cell cycle regulation, and genomic instability, expressed as chromosome breakage, gene amplification, and aneuploidy. An understanding of these mechanisms not only may lead to insights into carcinogenesis but ultimately may help us to interpret results of chromosome aberration tests and to develop a rational assessment of the degree of human risk implied by a positive aberration test.