Non-random distribution of aberrations and identification with C- and G-bindings of the position of breakage points on muntjac chromosomes induced by mitomycin C,bromodeoxyridine and hydroxylamine

The analysis of chromosomes from muntjac after treatment of its lymphocyte cultures with 3 chemical mutagens having different base-pair affinities and modes of action, namely mitomycin C (MC), 5-bromodeoxyuridine (BUdR) and hydroxylamine hydrochloride (HA), with G- and C-band staining displayed non-random distribution of chemically specific damage points on them. The randomness of the involvement of each site on the chromosomes was examined by assuming an expected value calculated on the basis of its relative mitotic length. The observation revealed that a large fraction of MC-induced aberrations was preferentially located in the C-band positive constitutive heterochromatin, especially in the long “neck-like” centromeric region of the X-chromosome. On the chromosomal arms, the light G-bands were involved in aberrations either in proportion to or higher than that expected. When the cells were treated with BUdR, the dark G-bands on all the chromosomes of the complement were the preferred sites, displaying statistically significant higher numbers of aberrations. A singe “hot-spot” for induced damage on 1 mid-q was also recorded. HA induced a very high frequency of damage in the secondary constriction regions of the chromosome pairs 1, X and Y₂, and the frequency was slightly lower than this in the centromeres of 1, 2 and X chromosomes.The observation of specific distribution of damage points induced by the 3 chemicals leads to the suggestion that, though the effect of a chemical on chromosome segments depends on several factors, each being partially responsible for the end result, it is perhaps primarily decided by the chemical's base-pair affinity and mode of action.A large variety of chemicals induce, in chromosomes, aberrations that are often distributed non-randomly. The non-random distribution of the chemically induced aberrations was noted even before the discovery of banding techniques, but with the use of conventional staining the identification of the exact location of induced break points, except for a few specific landmarks such as centromeres or secondary constrictions, was difficult and often unreliable too. Therefore, by using various banding techniques as a tool, a much more accurate assessment of the induced break points could be made. Several studies suggest that the involvement of specific chromosomes and/or chromosome segments are probably dependent upon the chemical used (Ayrand et al, 1976; Kaina, 1977; Kucerova and Polivkova, 1976; Morad et al., 1973; Morad and Zavahri, 1977; Reeves and Margoles, 1974). Meyne et. (1979) have suggested that, in addition to the nature of the chemicals used, the organization of chromosomes may also be responsible for the localized aberrations. To examine these points further, it was considered of interest to compare the extent of sensitivity of different chromosomal segments identified with banding techniques, after exposure to certain chemicals having different modes of action and base-pair affinities.In the present study, we compared the location of damage points on the chromosomes of the Indian barking deer Muntiacus muntjak, induced by 3 chemicals, namely (1) mitomycin C (MC), an antibiotic that acts by forming cross links with guanines between the complementary strands (Iyer and Szybalski, 1963), (ii) 5-bromodeoxyuridine (BUdR), a base analogue which is incorporated with concomitant thymine replacement into the DNA of mammalian cells (Djordjevic and Szybalski, 1960) and causes mutagenesis through a maispairing mechanism (Drake, 1970; Witkin and Parisi, 1974; Hutchinson and Stein, 1977; Rydberg, 1977), and (ii) hydroxylamine hydrochloride (HA), a reducing agent which reacts mainly with the cytosine moiety of the DNA by aminating only the C-4 atoms (Freese et al., 1961).     

Chromosome studies in plutonium workers

Chromosome analyses have been performed on peripheral blood lymphocytes from 54 men with estimates of plutonium body burdens in excess of 296 Bq. Both stable and unstable aberrations were scored using a banding technique and breakpoints noted. In discussing the significance of aberration frequencies the relative proportions of the different types of aberration and their distribution have been considered and account has been taken of external radiation exposure. It is suggested that significant depositions of plutonium do cause an increase in chromosome aberrations. The distribution of the breakpoints in the controls showed an excess in chromosomes 7 and 14. The formation and survival of radiation-induced breakpoints was randomly distributed amongst the chromosomes according to length. The distribution of the breakpoints within the chromosomes showed an excess in the centromeres and telomeres. Possible hot spots occurred in some of these regions and also in certain bands of the intermediate regions of the chromosomes.     

Genetic characterization of a reciprocal translocation present in a widely grown barley variety

Artificially induced translocation stocks have been used to physically map the barley genome; however, natural translocations are extremely uncommon in cultivated genotypes. Albacete is a barley variety widely grown in recent decades in Spain and carrying a reciprocal translocation which obviously does not affect its agronomical fitness. This translocation has been characterized by a combination of cytological and molecular genetic approaches. Firstly, recombination frequencies between markers on chromosomes 1H and 3H were estimated to determine the boundaries of the reciprocal interchange. Secondly, 1H-3H wheat barley telosome addition lines were used to assign selected markers to chromosome arms. Thirdly, fluorescence in situ hybridization (FISH) with rDNA probes (5S and 18S-5.8S-26S) and microsatellite probes [(ACT)(5), (AAG)(5) and (CAG)(5)] was used to determine the locations of the translocation breakpoints more precisely. Fourthly, fine-mapping of the regions around the translocation breakpoints was used to increase the marker density for comparative genomics. The results obtained in this study indicate that the translocation is quite large with breakpoints located on the long arms of chromosomes 1H and 3H, between the pericentromeric (AAG)(5) bands and above the (ACT)(5) interstitial distal bands, resulting in the reciprocal translocation 1HS.1HL-3HL and 3HS.3HL-1HL. The gene content around the translocation breakpoints could be inferred from syntenic relationships observed among different species from the grass family Poaceae (rice, Sorghum and Brachypodium) and was estimated at approximately 1,100 and 710 gene models for 1H and 3H, respectively. Duplicated segments between chromosomes Os01 and Os05 in rice derived from ancestral duplications within the grass family overlap with the translocation breakpoints on chromosomes 1H and 3H in the barley variety Albacete.     

Non-random intrachromosomal distribution of chromatid aberrations induced by X-rays,alkylating agents and ethanol in Vicia faba

A reconstructed karyotype of Vicia faba with all chromosomes individually distinguishable was treated with triethylene melamine (TEM), cytostasan (CYT) (a new benzimidazol nitrogen mustard), mitomycin C (MI), ethanol (EA) and X-rays. The distribution within chromosomes of induced chromatid abberations was non-random for all agents. The number of segments involved in aberration clustering corresponded to the number of sites representing constitutive heterochromatin, or the regions immediately adjacent to these, as evidenced by the position of Giemsa marker bands. Which of these potential regions of aberration clustering reacted with preferential involvement in aberrations was, in part at least, dependent upon the inducing agent used. It is argued that this may be due to differences in the base composition and/or molecular conformation of heterochromatic regions. Unexpectedly, the distribution pattern of chromatid aberrations induced by mitomycin C was found to be different from those after treatment with the alkylating agents TEM and cytostasan although mitomycin C is assumed to induce aberrations via alkylation. If mitomycin C-induced aberrations are indeed due to alkylation, this indicates that different alkylating agents do not necessarily result in identical patterns of abberation clustering. The other two alkylating agents and ethanol resulted in similar patterns of preferential distribution of abberations. X-Ray induced chromatid aberrations also showed a non-random intrachromosomal distribution, but the clustering was less pronounced than after treatment with the chemical agents.     

Reconstruction of the female Gorilla gorilla karyotype using 25-color FISH and multicolor banding (MCB)

The origin of the human and great ape chromosomes has been studied by comparative chromosome banding analysis and, more recently, by fluorescence in situ hybridization (FISH), using human whole-chromosome painting probes. It is not always possible, however, to determine the exact breakpoints and distribution or orientation of specific DNA regions using these techniques. To overcome this problem, the recently developed multicolor banding (MCB) probe set for all human chromosomes was applied in the present study to reanalyze the chromosomes of Gorilla gorilla (GGO). While the results agree with those of most previous banding and FISH studies, the breakpoints for the pericentric inversion on GGO 3 were defined more precisely. Moreover, no paracentric inversion was found on GGO 14, and no pericentric inversions could be demonstrated on GGO 16 or 17.     

The sites of radiation induced-breakage in human lymphocyte chromosomes, determined by quinacrine fluorescence

We have examined the distribution of 298 radiation-induced breakpoints in human chromosomes by quinacrine fluorescence. Very little damage was discovered which would not have been detectable with simple staining methods. The data suggest an excessive number of breaks in chromosomes 3 and a deficit in No. 16. The participation of chromosomes in rearrangements appears to be proportional to chromosome length. Within chromosome arms, breakpoints are selectively placed in telomeric regions.     

The distribution of randomly recovered X-ray-induced sex-linked genetic effects in Drosophila melanogaster

Cytogenetic analysis of more than 1500 randomly recovered lethal X chromosomes derived from 2000 and 3000 r X-ray exposures of post-meiotic male germ cells has made possible a plot of the distribution in different regions of the X chromosome of: (1) gene mutations associated with cytologically normal chromosomes, (2) mutations associated with chromosomal rearrangement breakpoints, (3) deficiencies, and (4) rearrangement breakpoints whether or not they are associated with mutations. The distribution of point mutations, vital loci and rearrangement breakpoints in different regions of the X chromosome is not proportional to either the number of bands or the relative DNA content. Further, the density of vital loci (those capable of mutating to a lethal allele) is quite different in some regions as compared to others. For example, vital loci in the 3AB region, which has been thoroughly studied by Judd and others, are at least as numerous as bands; whereas, the 3CD region, equally long, has only two vital loci. Other regions densely populated with vital loci include 1B, 1F-2A, 10A, 11A, and 19EF; sparsely populated regions include 6EF and 10B-10E. It seems reasonable to conclude that the recovered X-ray-induced mutants available for analysis do not represent a random sample of those initially induced in the exposed male germ cells.     

The distribution of radiation-induced breaks in the chromosomes of irradiated subjects

Distribution of radiation-induced breakpoints in chromosomes and its bands in persons recovered from acute radiation sickness and personnel from Chernobyl NPP were investigated using G-banding staining. The frequency of damaged bands and breakpoints in groups exposed to radiation was significantly higher as compared with the control group. It was shown that in exposed to radiation persons damage depends on its length. Most frequently damaged bands in the observed groups were determined. The G-negative bands and telomeres of chromosomes were more sensitive to radiation.     

Is mammalian chromosomal evolution driven by regions of genome fragility?

Background

A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats.

Results

Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence.

Conclusion

These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity.     

In vitro and in vivo extrapolations of genotoxin exposures: consideration of factors which influence dose-response thresholds

The concept of a threshold of activity of a genotoxic agent is primarily based upon considerations of protective mechanisms and multiple cellular targets, which require inactivation before a toxic response is produced. In this paper, we have considered and evaluated the influences of compound metabolism, DNA lesion formation, mutation induction and sequence content, aneuploidy induction and the influence of repair enzymes upon genetic endpoints produced by both DNA reactive chemicals and by those chemicals which modify non-DNA cellular targets. Thresholds of activity have been evaluated by critical analysis of the published literature and original data analysing both the role of sequence context upon point mutation induction and DNA repair mechanisms upon the sensitivity of cultured cells to the induction of aneuploidy. In the case of DNA reactive chemicals, the presence of a threshold of chemical activity will be dependent upon cellular activities such as those of the Phase II enzymes reducing the activity of chemicals before lesion formation takes place and/or those of the DNA repair enzymes which reduce the proportion of DNA lesions which are processed into DNA sequence changes. Under such conditions, a given exposure of a DNA reactive chemical does not produce a linear or semi-linear increase in DNA lesions or in mutation frequency. However, even when these protective mechanisms are overwhelmed by the high exposures of genotoxic chemicals the biological effects of a genotoxin may be influenced by the sequence context of the gene under consideration. Here, we demonstrate that point mutations are detected at relatively higher frequencies in the non-coding introns compared with the coding exons. Many of the base changes detected in the exons do not produce amino acid changes in the proteins coded for by the genes being monitored for mutation induction. Both sequence context and the types of base changes induced may provide a "buffering" effect reducing the biological consequences of mutation induction. Spindle damaging chemicals, such as colcemid and vinblastine, induce aneuploidy by modifying the numbers of spindle fibres which regulate the segregation of chromosomes during mitosis and meiosis. The redundancy of spindle fibres in the dividing mammalian cell leads to the prediction that only chemical exposures which damage most, if not all, of the fibres will lead to the induction of polyploidy and/or aneuploidy. Such predicted thresholds of chemical activity can be observed when both chromosome loss and non-disjunction are measured in wild type cultures. However, we observed a substantial increase in sensitivity to aneugenic chemicals when measurements were made in primary cell cultures derived from xerodoma pigmentosum and trichothiodystrophy patients. Further studies are necessary to evaluate the consequences of the genetic background of tester strains upon the nature of the dose-response curve of aneugenic chemicals.     

Nineteen of 26 cellular oncogenes precisely localized in the human genome map to one of the 83 bands involved in primary cancer-specific rearrangements

Summary A total of 83 bands have been found to be specifically involved in primary structural chromosome rearrangements in human cancer. We have compared the distribution of these cancer-specific breakpoints with the chromosomal sites of the 26 cellular oncogenes currently mapped to individual bands within the human genome. Nineteen of the 26 oncogenes are localized in cancer-associated bands. This clustering of oncogene sites and cancer breakpoints is statistically highly significant (P=0.0000012).     

The action of N-methyl-N-nitrosourea on non-established human cell lines in vitro. II. Non-random distribution of chromatid aberrations in diploid and Down's cells.

Chromatid gaps, breaks and aberrations involved in interchanges induced by N-methyl-N-nitrosourea (MNU) were found non-randomly distributed on individual chromosomes and chromosome segments (G bands) both in human diploid fibroblasts with trisomy 21 cultured in vitro. Aberration events were located exclusively in pale G bands. Considering cells in the first post-treatment mitosis, the pattern of aberration distribution, as revealed by the position of hot spots, varied with recovery time and was different in diploid and Down's cells. In comparison with diploid cells, the X chromosomes of Down's cells were not involved in aberrations. Despite the higher aberration frequencies of Down's cells, the number of hot spots and the proportion of aberrations located in hot spots were not increased in this cell type. Therefore, the increased chromosomal sensitivity to MNU of Down's cells does not reflect an increased sensitivity of special chromosomes or chromosome sites.     

Analysis of bleomycin- and cytosine arabinoside-induced chromosome aberrations involving chromosomes 1 and 4 by painting FISH

The genomic frequency of chromosomal aberrations obtained by chromosome painting is usually extrapolated from the observed frequency of aberrations by correcting for the DNA content of the labelled chromosomes. This extrapolation is based upon the assumption of random distribution of breakpoints from which aberrations are generated. However, the validity of this assumption has been widely questioned. While extensive investigations have been performed with ionizing radiation as chromosome breaking agent, little efforts have been done with chemical clastogens. In order to investigate interchromosomal differences in chemically-induced chromosome damage, we have used multicolour chromosome painting to analyse bleomycin-induced aberrations involving chromosomes 1 and 4, two chromosomes that differ in gene density. In addition, we have measured the effect of cytosine arabinoside upon the repair of bleomycin-induced DNA damage in chromosomes 1 and 4. Our results show that these chromosomes are equally sensitive to the clastogenic effect of bleomycin with a similar linear dose-effect relationship. However, the high gene density chromosome 1 appeared to be more sensitive to repair inhibition by Ara-C than chromosome 4. This enhanced sensitivity to repair inhibition in chromosome 1 could be mediated by preferential repair of open chromatin and actively transcribed regions.     

Heterogeneity of pericentric inversions of the human y chromosome

Pericentric inversions of the human Y chromosome (inv(Y)) are the result of breakpoints in Yp and Yq. Whether these breakpoints occur recurrently on specific hotspots or appear at different locations along the repeat structure of the human Y chromosome is an open question. Employing FISH for a better definition and refinement of the inversion breakpoints in 9 cases of inv(Y) chromosomes, with seemingly unvarying metacentric appearance after banding analysis, unequivocally resulted in heterogeneity of the pericentric inversions of the human Y chromosome. While in all 9 inv(Y) cases the inversion breakpoints in the short arm fall in a gene-poor region of X-transposed sequences proximal to PAR1 and SRY in Yp11.2, there are clearly 3 different inversion breakpoints in the long arm. Inv(Y)-types I and II are familial cases showing inversion breakpoints that map in Yq11.23 or in Yq11.223, outside the ampliconic fertility gene cluster of DAZ and CDY in AZFc. Inv(Y)-type III shows an inversion breakpoint in Yq11.223 that splits the DAZ and CDY fertility gene-cluster in AZFc. This inversion type is representative of both familial cases and cases with spermatogenetic impairment. In a further familial case of inv(Y), with almost acrocentric morphology, the breakpoints are within the TSPY and RBMY repeat in Yp and within the heterochromatin in Yq. Therefore, the presence of specific inversion breakpoints leading to impaired fertility in certain inv(Y) cases remains an open question.     

Comparative radiation hybrid map of canine chromosome 1 incorporating SNP and indel polymorphisms

We report a comparative map of canine chromosome 1 (CFA1) incorporating single nucleotide polymorphisms (SNPs) and insertion/deletion (indel) polymorphisms, developed by using cross-species primers, radiation hybrid analysis, and pool-and-sequence identification of genetic variations. Fifty-five genes were chosen with relatively even spacing (approximately 3 Mb between the human homologues) and were mapped to CFA1, with 49 of these being new assignments. Evolutionary chromosomal breakpoints between CFA1 and the corresponding human chromosomes (HSA6, HSA9, HSA18, and HSA19) were located within 1 to 5 Mb based upon the human genome sequence. The process of identifying the evolutionary chromosomal breakpoints between CFA1 and the relevant human chromosomes led to an improvement in the comparative maps of CFA7, CFA12, and CFA29 through the mapping of 21 additional genes. A manual pool-and-sequence method was used to identify 79 SNPs, 9 small indels, 7 simple tandem repeats, and 2 polymorphic SINE insertions within the genes mapped. The cross-species primers can also be used in the manner described here to improve the comparative maps for other mammalian species.     

Banding pattern analysis of initial structural chromosome alterations induced by n-methyl-n'-nitro-n-nitrosoguanidine in Syrian hamster cells

Cultured secondary Syrian hamster embryo cells exposed to 0.5 N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) microgram/ml medium exhibited chromatid type of aberrations consisting of gaps, breaks and exchanges. Although no specific chromosome or chromosome segment was preferentially affected, chromosomes belonging to the larger groups tended to more often involved. G-band analysis demonstrated that 80% of the lesions occurred in negative bands, 9% involved the centromere, 3% were on non-banded heterochromatin, and approximately 8% of the lesions could not be definitely categorized by G-band analysis. Whether the lesions occur at positive bands or at the interface between negative and positive bands is difficult to discern by the G-band resolution. The Y chromosome compared to autosomes of similar size rarely had lesions. X chromosome damage was found in both the euchromatic and heterochromatic arms. However, both sex chromosomes, as well as an autosome (E20) which is heterochromatic on its long arm, were not found joined to the chromatids of other chromosomes, further emphasizing that chromosomes with large heterochromatic areas are isolated in terms of chromatid exchange events. The analysis of MNNG induced chromosome damage indicates that the negative bands are the primary site of damage and points of exchange.     

Use of a human X mouse hybrid cell line to detect aneuploidy induced by environmental chemicals

A short-term assay utilizing a human/mouse monochromosomal hybrid cell line R3-5, to detect chemically induced aneuploidy in mammalian cells is described. A single human chromosome transferred into mouse cells was used as a cytogenetic marker to quantitate abnormal chromosome segregation following chemical treatment. The human chromosome present in the mouse cells can be readily identified by differential staining procedures. The frequency of cells containing 0 or 2 human chromosomes in the progeny of chemically treated monochromosomal hybrid cells provided a direct measure of aneuploidy. We tested the sensitivity of the proposed system with 3 model chemicals (colcemid, cyclophosphamide and benomyl) known to induce numerical or structural changes in chromosomes. The frequency of an abnormal segregation of the human chromosome was found to be dose dependent and consistently higher than controls. This system has the capability to detect gain as well as loss of a chromosome resulting from nondisjunction or other mechanisms leading to aneuploidy.     

Genetic effects of combined chemical-X-ray treatments in male mouse germ cells

Several studies have shown that the yield of genetic damage induced by radiation in male mouse germ cells can be modified by chemical treatments. Pre-treatments with radio-protecting agents have given contradictory results but this appears to be largely attributable to the different germ cell stages tested and dependent upon the level of radiation damage induced. Pre-treatments which enhance the yield of genetic damage have been reported although, as yet, no tests have been conducted with radio-sensitizers. Another form of interaction between chemicals and radiation is specifically found with spermatogonial stem cells. Chemicals that kill cells can, by population depletion, substantially and predictably modify the genetic response to subsequent radiation exposure over a period of several days, or even weeks. Enhancement and reduction in the genetic yield can be attained, dependent upon the interval between treatments, with the modification also varying with the type of genetic damage scored. Post-treatment with one chemical has been shown to reduce the genetic response to radiation exposure.     

Molecular Definition of Pericentric Inversion Breakpoints Occurring during the Evolution of Humans and Chimpanzees

High-resolution G-banding analysis has demonstrated remarkable morphological conservation of the chromosomes of the Hominidae family members (humans, chimpanzees, gorillas, and orangutans), with the most notable differences between the genomes appearing as changes in heterochromatin distribution and pericentric inversions. Pericentric inversions may have been important for the establishment of reproductive isolation and speciation of the hominoids as they diverged from a common ancestor. Here the previously published primate karyotype comparisons, coupled with the resources of the Human Genome Project, have been used to identify pericentric inversion breakpoints seen when comparing the human karyotype to that of chimpanzee. Yeast artificial chromosome (YAC) clones were used to detect, by fluorescencein situhybridization, five evolutionary pericentric inversion breakpoints present on the chimpanzee chromosome equivalents of human chromosomes 4, 9, and 12. In addition, two YACs from human 12p that detect a breakpoint in chimpanzee detect a similar rearrangement in gorilla.