Distribution and localisation of induced breaks in the chromosomes of Bellevalia. 3. Sodium nitrite

Summary Nitrous acid induces fragmentation of chromosomes and only very few translocations in Bellevalia romana (2n=8). A total of 1098 breaks is induced by 1×10^-3, 1,5×10^-4 and 1,5×10^-5 M NaNO₂ at pH 4,5. Root tips were fixed at 24, 48 and 72 hours after treatment for 1 hour.The percentage of breaks increases with time between treatment and fixation; it reaches its highest level at 1,5×10^-4 M, which dose coincides with the lowest mitotic rate.A dose influence on the distribution of breaks among the centromeres and the chromosome arms was observed. Consistent with the effect of other agents the highest number of breaks was in the A- the lowest, however, in the D-chromosome.The distribution of breaks on the different chromosome arms was homogeneous for all fixations. As observed previously the breakage frequency was not proportional to the arm length.The distribution of breaks on the proximal, median and distal sections of the chromosome arms is significantly different from random distribution.The nitrous acid-induced pattern of breaks is significantly different from that induced by methylating (MMS+NMU) and ethylating agents (DES+NEU).The known primary chemical reaction of nitrous acid and alkylating agents with DNA are inadequate alone in explaining the different patterns of breaks. More information is needed regarding the processes following these primary reactions.In conclusion, several possible objections against the technique of localizing breaks are shown to be non-valid.     

Localization of translocation breakpoints in somatic metaphase chromosomes of barley

Karyotype analyses based on staining by acetocarmine followed by Giemsa N-banding of somatic metaphase chromosomes of Hordeum vulgare L. were carried out on 61 reciprocal translocations induced by X-irradiation. By means of computer-based karyotype analyses all of the 122 breakpoints could be localized to defined sites or segments distributed over the seven barley chromosomes. The pre-definition of translocations with respect to their rearranged chromosome arms from other studies rendered it possible to define the break positions even in translocations having exchanged segments equal in size and the breakpoints located distally to any Giemsa band or other cytological marker. The breakpoints were found to be non-randomly spaced along the chromosomes and their arms. All breaks but one occurred in interband regions of the chromosomes, and none of the breaks was located directly within a centromere. However, short and long chromosome arms recombined at random. An improved tester set of translocations depicting the known break positions of most distal location is presented.     

Susceptibility of heterochromatin to aphidicolin-induced chromosomal breakage

The distribution of aphidicolin-induced chromosomal lesions was analyzed to determine the relative breakage susceptibility of euchromatin and heterochromatin in the cactus mouse, Peromyscus eremicus. The observed breakage was tested against expected distributions corresponding to the karyotypic proportions of autosomal euchromatin, autosomal heterochromatin, X-chromosomal euchromatin, and X-chromosomal heterochromatin. The distribution of induced breakage was independent of sex but dependent on the individual. In all individuals, there was a highly significant (P0.0001) deficiency in the number of breaks observed as compared to expected in autosomal heterochromatin. Sparse observations in the X chromosome and the absence of breaks in the Y chromosome precluded valid statistical tests of the sex-chromosomal distribution of induced breakage. These data indicate that the autosomal heterochromatin of Peromyscus is resistant to aphidicolin-induced chromosomal breakage and argue against a simple relationship between late replication and a general mechanism for chromosomal fragility.     

Synthesis of an attached autosome,C(3)RM,inDrosophila pseudoobscura

Drosophila pseudoobscura has three acrocentric autosomes. In the experiments reported, homologous arms of the third chromosome were attached to the same centromere. This is a reversed metacentric compound third chromosome, denoted by C(3)RM. This compound chromosome is relatively fertile in within-strain crosses (ca. 50% egg hatch) but sterile when outcrossed to a normal karyotype. When constructing translocations for this experiment, the behavior of the Y-autosome translocations suggested that this species can tolerate more Y chromosome deficiency while retaining fertility than canDrosophila melanogaster. Finally, there were no Robertsonian exchanges observed among the 96 autosome-autosome translocations analyzed cytologically.     

Nature and distribution of chromosomal intertwinings in Saccharomyces cerevisiae.

To elucidate yeast chromosome structure and behavior, we examined the breakage of entangled chromosomes in DNA topoisomerase II mutants by hybridization to chromosomal DNA resolved by pulsed-field gel electrophoresis. Our study reveals that large and small chromosomes differ in the nature and distribution of their intertwinings. Probes to large chromosomes (450 kb or larger) detect chromosome breakage, but probes to small chromosomes (380 kb or smaller) reveal no breakage products. Examination of chromosomes with one small arm and one large arm suggests that the two arms behave independently. The acrocentric chromosome XIV breaks only on the long arm, and its preferred region of breakage is approximately 200 kb from the centromere. When the centromere of chromosome XIV is relocated, the preferred region of breakage shifts accordingly. These results suggest that large chromosomes break because they have long arms and small chromosomes do not break because they have small arms. Indeed, a small metacentric chromosome can be made to break if it is rearranged to form a telocentric chromosome with one long arm or a ring with an "infinitely" long arm. These results suggest a model of chromosomal intertwining in which the length of the chromosome arm prevents intertwinings from passively resolving off the end of the arm during chromosome segregation.     

Are aneuploidy and chromosome breakage caused by a CINgle mechanism?

Genetic instability is a hallmark of cancer. Most tumors show complex patterns of translocations, amplifications, and deletions, which have occupied scientists for decades. A specific problem arises in carcinomas with a genetic defect termed chromosomal instability; these solid tumors undergo gains and losses of entire chromosomes, as well as segmental defects caused by chromosome breaks. To date, the apparent inconsistency between intact and broken chromosomes has precluded identification of an underlying mechanism. The recent identification of centromeric breaks alongside aneuploidy in cells with spindle defects indicates that a single mechanism could account for all genetic alterations characteristic of chromosomal instability. Since a poorly controlled spindle can cause merotelic attachments, kinetochore distortion, and subsequent chromosome breakage, spindle defects can generate the sticky ends necessary to start a breakage-fusion-bridge cycle. The characteristic breakpoint of spindle-generated damage, adjacent to the centromere, also explains the losses and gains of whole chromosome arms, which are especially prominent in low-grade tumors. The recent data indicate that spindle defects are an early event in tumor formation, and an important initiator of carcinogenesis.     

An efficient screening for terminal deletions and translocations of barley chromosomes added to common wheat

As a prerequisite to determine physical gene distances in barley chromosomes by deletion mapping, a reliable, fast and inexpensive approach was developed to detect terminal deletions and translocations in individual barley chromosomes added to the chromosome complement of common wheat. A refined fluorescence in situ hybridization (FISH) technique subsequent to N-banding made it possible to detect subtelomeric repeat sequences (HvT01) on all 14 chromosome arms of barley. Some chromosome arms could be distinguished individually based on the number of FISH signals or the intensity of terminal FISH signals. This allowed the detection and selection of deletions and translocations of barley chromosomes (exemplified by 7H and 4HL), which occurred in the progeny of the wheat lines containing a pair of individual barley chromosomes (or telosomes) and a single so-called gametocidal chromosome (2C) of Aegilops cylindrica. This chromosome is known to cause chromosomal breakage in the gametes in which it is absent. Terminal deletions and translocations in barley chromosomes were easily recognized in metaphase and even in interphase nuclei by a decrease in the number of FISH signals specific to the subtelomeric repeat. These aberrations were verified by genomic in situ hybridization. The same approach can be applied to select deletions and translocations of other barley chromosomes in wheat lines that are monosomic for the Ae. cylindrica chromosome 2C.     

Analysis of translocations observed in three different populations. I. Reciprocal translocations

A sample of 437 reciprocal translocations was classified into three groups according to their method of ascertainment (Group I = couples with repeated abortions; Group II = karyotypically unbalanced carriers; Group III = balanced translocation heterozygotes). Statistical analysis showed that the distributions of chromosome breaks observed in the three groups could not be accounted for by chromosome arm length alone. In couples with repeated abortions, an excess of breaks in 7p, 17p, and 22q was found, whereas in the balanced translocation heterozygotes an excess of breaks was found only in 11q. An excess of breaks was found in arms 9p, 14p, 18p, 18q, 21q, and 22q in karyotypically unbalanced probands. A significant decrease of breaks in the medial chromosome regions was accompanied by a concomitant increase in the terminal regions in all groups. The three groups demonstrated different distributions of chromosome arm involvement in the observed translocations. Balanced translocation heterozygotes had the highest frequency of large (greater than the length of 4p) translocated segments and an excess in the frequency of large-large translocations, whereas karyotypically unbalanced probands had the highest frequency of small (shorter than 21q) translocations and an excess in the frequency of small-small translocations. For each type of chromosomal imbalance observed, the balanced translocation heterozygotes demonstrated the greatest potential imbalance and the karyotypically unbalanced probands the least.     

Die Erzeugung von Chromatidenbrüchen durch Coffein in Leukocytenkulturen des Menschen

The induction of chromosome (chromatid) breakage in human leukocyte cultures by treatment of the cells with 1% (2 hrs) caffeine is described.

1. 1.
   Caffeine induced breakage is dependent on the time of exposure of the cells to caffeine. Treatment in the first two hours of cultivation results in a low number of chromatid breaks in the mitosis following the treatment. Maximal breakage is induced by exposure of the cells in the middle and late G-1-phase. Less frequent breakage is induced in the last part of the S-phase, there is almost no effect on the G-2-phase if there is no DNA synthesis following treatment and preceding observation.     
   
   

C,Q and H-banding in the analysis of Y chromosome rearrangements in Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae)

In Lucilia cuprina C-banding produces procentric bands on all autosomes and deep staining over most of the X and Y chromosomes which conciderably facilitates the analysis of complex Y chromosome rearrangements. The Y chromosome is generally darkly C-banded throughout while in the X chromosome a pale staining segment is found in the distal portion of the long arm. Modulation of the banding reaction results in grey areas in both X and Y. When C-banding is compared with allocycly it is clear that not all heteropycnotic regions in the sex chromosomes C-band to the same extent. Secondary constrictions in the short arms of both X and Y chromosomes are clearly revealed by C-banding, the X satellite being polymorphic for size.— Q-banding results in a brightly fluorescing band in the short arm of structurally normal Y chromosomes. This band loses its fluorescence in some translocations, probably through a position effect. Hoechst 33258 staining does not produce any brightly fluorescing bands.     

Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements

Inverted DNA repeats are known to cause genomic instabilities. Here we demonstrate that double-strand DNA breaks (DSBs) introduced a large distance from inverted repeats in the yeast (Saccharomyces cerevisiae) chromosome lead to a burst of genomic instability. Inverted repeats located as far as 21 kb from each other caused chromosome rearrangements in response to a single DSB. We demonstrate that the DSB initiates a pairing interaction between inverted repeats, resulting in the formation of large dicentric inverted dimers. Furthermore, we observed that propagation of cells containing inverted dimers led to gross chromosomal rearrangements, including translocations, truncations, and amplifications. Finally, our data suggest that break-induced replication is responsible for the formation of translocations resulting from anaphase breakage of inverted dimers. We propose a model explaining the formation of inverted dicentric dimers by intermolecular single-strand annealing (SSA) between inverted DNA repeats. According to this model, anaphase breakage of inverted dicentric dimers leads to gross chromosomal rearrangements (GCR). This "SSA-GCR" pathway is likely to be important in the repair of isochromatid breaks resulting from collapsed replication forks, certain types of radiation, or telomere aberrations that mimic isochromatid breaks.     

Chromosomal rearrangements in Plantago insularis Eastw.

Seeds of Plantago insularis Eastw. which were irradiated with gamma rays yielded 37–67% semi-sterile plants. Twenty-four out of sixty-four of these plants were heterozygous for one or more chromosomal rearrangements. Twothirds of these were translocations, and one-third were inversions. Homozygous lines for four translocations were established. The karyotypes of these provide chromosome markers either at pachynema or in mitotic divisions, or both.Breakage positions were usually located within hetrochromatic segments or at the ends of heterochromatic regions (72.6% of all breaks), and half of all breaks occurred at the juncture of the centromere with the proximal heterochromatin. The consequences of proximal breakage were non-random, in that 93% of such breaks resulted in translocations and only 7% in inversions, whereas more than half of breaks in non-centromeric regions became involved in inversions.The individual chromosomes differed in the types of breakage and of aberrations produced, and these differences appeared correlated with length ratios of heterochromatic segments flanking the centromeres.The research for this paper was supported by National Science Foundation Grant Number GB 5713X.     

Chromosome and nucleotide sequence differentiation in genomes of polyploid Triticum species

Summary The nature of genome change during polyploid evolution was studied by analysing selected species within the tribe Triticeae. The levels of genome changes examined included structural alterations (translocations, inversions), heterochromatinization, and nucleotide sequence change in the rDNA regions. These analyses provided data for evaluating models of genome evolution in polyploids in the genus Triticum, postulated on the basis of chromosome pairing at metaphase I in interspecies hybrids.The significance of structural chromosome alterations with respect to reduced MI chromosome pairing in interspecific hybrids was assayed by determining the incidence of heterozygosity for translocations and paracentric inversions in the A and B genomes of T. timopheevii ssp. araraticum (referred to as T. araraticum) represented by two lines, 1760 and 2541, and T. aestivum cv. Chinese Spring. Line 1760 differed from Chinese Spring by translocations in chromosomes 1A, 3A, 4A, 6A, 7A, 3B, 4B, 7B and possibly 2B. Line 2541 differed from Chinese Spring by translocations in chromosomes 3A, 6A, 6B and possibly 2B. Line 1760 also differed from Chinese Spring by paracentric inversions in arms 1AL and 4AL whereas line 2541 differed by inversions in 1BL and 4AL (not all chromosomes arms were assayed). The incidence of structural changes in the A and B genomes did not coincide with the more extensive differentiation of the B genomes relative to the A genomes as reflected by chromosome pairing studies.To assay changing degrees of heterochromatinization among species of the genus Triticum, all the diploid and polyploid species were C-banded. No general agreement was observed between the amount of heterochromatin and the ability of the respective chromosomes to pair with chromosomes of the ancestral species. Marked changes in the amount of heterochromatin were found to have occurred during the evolution of some of the polyploids.The analysis of the rDNA region provided evidence for rapid fixation of new repeated sequences at two levels, namely, among the 130 bp repeated sequences of the spacer and at the level of the repeated arrays of the 9 kb rDNA units. These occurred both within a given rDNA region and between rDNA regions on nonhomologous chromosomes. The levels of change in the rDNA regions provided good precedent for expecting extensive nucleotide sequence changes associated with differentiation of Triticum genomes and these processes are argued to be the principal cause of genome differentiation as revealed by chromosome pairing studies.     

Chromosome-breakage genomic instability and chromothripsis in breast cancer

Background

Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome.

Results

We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers.

Conclusions

Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-579) contains supplementary material, which is available to authorized users.     

A model for somatic pairing derived from somatic crossing over with third chromosome rearrangements in Drosophila melanogaster

Summary X-ray induced crossing-over between the left arms of third chromosome pairs heterozygous for rearrangements was used to measure the somatic pairing of these arms. mwh spots were scored in the wing blades. A significantly reduced number of crossover spots is found in flies heterozygous for inversions or translocations located in the 3L arm. This decrease from control frequencies was experimentally demonstrated to be due to inviability of some crossover spots which are aneuploid as a result of crossing-over within the inverted sequence or between the translocation piece and its centromere. By the same token, some euploid crossover spots are produced by crossing-over outside of the inverted region or between the translocation breakpoint and the mwh locus. Thus, these results are evidence that the euchromatic non-centric portions of the 3L arms are somatically paired in the presence of rearrangements.A model of somatic pairing in which chromosomes are normally found in a hair pin configuration is proposed to account for these results and for some previous results with X-chromosomes which indicated that inversion heterozygotes did not pair somatically.Supported in part by USPHS grant GM 16096 to J.R.M.     

Cytogenetic characteristics of a population of Chironomus riparius Meigen 1804 (Diptera, Chironomidae) from a polluted Po river station

A population of Chironomus riparius from a Po river station near Moncalieri (a trace-metal polluted station) was studied. In this population was established a great variability of band structure of polytene chromosomes as well as paracentric heterozygous inversions, deletions, deficiencies, partial breaks, diploid chromosome fragments, and changes in functional activity and appearance of heterochromatin. In arms A through F, some bands had an increased size compared to the standard chromosomic map. Some bands appeared in a heterozygous or normal homozygous state or were amplified. In all arms, many condensed stable bands appeared in the decondensed state when compared to the standard map. Asynaptic zones in arms E and G as well as heterozygous Balbiani rings and NORs were established. Very often the 4th chromosome was almost completely heteropycnotic and looded like a pompon chromosome. For the first time in this species, a high frequency of ectopic pairings of different arms was observed. Telomeric regions involved in ectopic pairings had a granular appearance, as did some centromeres. The hypothesis is advanced that such a high frequency of structural rearrangements could be correlated with genomic distribution of specific mobile elements.     

Unusual supernumerary chromosomes: types encountered in a referred population,and high incidence of associated maternal chromosome abnormalities

Summary In a 6-year period 128 patients with supernumerary autosomes were identified in our laboratory. The majority had primary trisomy, but 19 (15%) had extra, unusual chromosomes, not just a normal chromosome present in an extra copy. Of these, 18 were complex and did not resemble any one part of the standard chromosome complement. There was a preponderance of females among the 19 cases. Chromosome analysis of the parents in the 14 most recent cases revealed maternal chromosome abnormalities in 11 (79%). Of these 11, eight mothers had balanced reciprocal translocations; nondisjunction led to the smaller of their translocation chromosomes being passed on as the supernumerary chromosome in their offspring. Thus, nondisjunction of maternal translocations accounts for a major proportion of the unusual supernumerary chromosomes found by our laboratory. Advanced maternal age was noted in this group of mothers. Three mothers had supernumerary chromosomes themselves. We conclude that unusual supernumerary chromosomes (1) are not rare among patients referred for chromosome studies; (2) are generally not simple products of breakage; (3) are very frequently the result of malsegregation of a balanced maternal reciprocal translocation; and (4) are very difficult to characterize unless a balanced parental translocation is identified. Parental karyotypes should be obtained whenever a patient has an extra, unusual chromosome.     

Translocations of chromosome 12

Summary Human chromosome 12 has been used as a model for studying the distributions of sites of induced and spontaneous breaks. The breakpoints were determined from (1) translocations involving chromosome 12, (2) spontaneous breaks in untreated cultures, (3) radiation-induced breaks, and (4) spontaneous breaks in Fanconi's anaemia.Statistical analysis showed discordance in the results both between the eleven individual bands and between the four assessments. Also, the distribution of breaks for all bands was significantly diferent from random in each assessment. Certain bands added considerable bias to the results, and when analysed individually, only four bands (p11.1, q13, q24, and p13) showed distributions over the four assessments that were significantly different from random. These four bands are Giemsa-negative bands, and two (p13 and q24) are adjacent to telomeres, while p11.4 is adjacent to the centromere. The fourth band, q13, is a known fragile site.It is concluded that bands adjacent to centromeres, which are not C-banded, are peculiarly sensitive to breakage. Telomeric bands are variable in their response to different conditions of breakage, and both the physical structure of the telomere and the specific gene sequences of individual telomeres are probably of importance in determining this response. The fragile site q13 responds as if breakage at this site is due to the base composition of the DNA.