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PubMed2005

Concurrent loss of chromosome arm 1p and chromosome 3 predicts a decreased disease-free survival in uveal melanoma patients.

PURPOSE: Uveal melanoma is a highly malignant disease with a mortality rate of 50% at 10 to 15 years. Previous studies have shown that chromosomal changes are associated with decreased survival of the patient. However, in these studies the small number of tumors analyzed did not allow robust statistical analysis. In the present study, the independent numerical changes in chromosomes 1, 3, 6, and 8 on disease-free survival (DFS) was assessed in a large series of patients with uveal melanoma. METHODS: One hundred twenty tumors from patients with uveal melanoma were analyzed for numerical changes in chromosomes 1, 3, 6, and 8, with cytogenetic analysis, fluorescent in situ hybridization, and/or comparative genomic hybridization. Data were correlated with disease outcome in univariate and multivariate analyses, by Kaplan-Meier and Cox regression analyses. RESULTS: At a mean follow-up time of 45 months, 42 patients had died or had metastatic disease. In the univariate analysis, loss of chromosome 3, gain of 8q, largest tumor diameter, or the presence of epithelioid cells was associated with a decreased DFS. In the multivariate analysis, the effect of monosomy 3 on survival was largely modified by changes in 1p36. Regarding all chromosomal changes, only the concurrent loss of the short arm of chromosome 1 and all of chromosome 3 was an independent prognostic parameter for disease-free survival (P < 0.001). CONCLUSIONS: In uveal melanoma, concurrent loss of the short arm of chromosome 1 and all of chromosome 3 is an independent predictor of decreased DFS.

Adult↗
PubMed2005

The program of sex chromosome pairing in meiosis is highly conserved across marsupial species: implications for sex chromosome evolution.

Marsupials present a series of genetic and chromosomal features that are highly conserved in very distant species. One of these features is the absence of a homologous region between X and Y chromosomes. According to this genetic differentiation, sex chromosomes do not synapse during the first meiotic prophase in males, and a special structure, the dense plate, maintains sex chromosome association. In this report we present results on the process of meiotic sex chromosome pairing obtained from three different species, Thylamys elegans, Dromiciops gliroides, and Rhyncholestes raphanurus, representing the three orders of American marsupials. We have investigated the relationships between the axial structures organized along sex chromosomes and the formation of the dense plate. We found that in the three species the dense plate arises as a modification of sex chromosomal axial elements, but without the involvement of other meiotic axial structures, such as the cohesin axes. Considering the phylogenetic relationships among the marsupials studied here, our data reinforce the idea that the dense plate emerged early in marsupial evolution as an efficient mechanism to ensure the association of the nonhomologous sex chromosomes. This situation could have influenced the further evolution of sex chromosomes in marsupials.

Animals↗
PubMed2005

Inducing rye 1R chromosome structural changes in common wheat cv. Chinese spring by the gametocidal chromosome 2C of Aegilops cylindrica.

To generate 1 R deletion and translocation lines, we introduced a 2C chromosome,which was derived from Aegilops cylindrica and was known to have a gametocidal function when added monosomically into common wheat cv. Chinese Spring (CS) and its derivative, into a wheat-rye 1R chromosome disomic addition line (CS-1R"). When the individuals with chromosome constitution 21" + 1R" + 2C' (2n = 45) were selfed, the 1R chromosome structural changes were found to be induced with high frequency (24.1%) among the progenies. By using C-banding and GISH analysis, we analyzed 1R structural changes in 46 F3 individuals, which came from 23 F2 plants. The rearranged 1R chromosomes could be characterized in about 85% of the F3 individuals. This included telosome 1RL (39.1%), iso-chromosome 1 RL (2.2%), whole arm translocation involving 1RL (32.6%), telosome 1RS (4.3%), iso-chromosome 1RS (4.3%), and 1R deletion mutant with break point in the long arm (2.2%). The mutant 1R lines obtained in this study will potentially be useful in mapping the chromosome locations of agronomically important genes located in 1R. This study also demonstrated that molecular markers might be used to identify wheat chromosome arm involved in translocation with 1R.

Chromosome Aberrations↗
PubMed1993

Maternal uniparental disomy for human chromosome 14, due to loss of a chromosome 14 from somatic cells with t(13;14) trisomy 14.

Uniparental disomy (UPD) for particular chromosomes is increasingly recognized as a cause of abnormal phenotypes in humans. We recently studied a 9-year-old female with a de novo Robertsonian translocation t(13;14), short stature, mild developmental delay, scoliosis, hyperextensible joints, hydrocephalus that resolved spontaneously during the first year of life, and hypercholesterolemia. To determine the parental origin of chromosomes 13 and 14 in the proband, we have studied the genotypes of DNA polymorphic markers due to (GT)n repeats in the patient and her parents' blood DNA. The genotypes of markers D14S43, D14S45, D14S49, and D14S54 indicated maternal UPD for chromosome 14. There was isodisomy for proximal markers and heterodisomy for distal markers, suggesting a recombination event on maternal chromosomes 14. In addition, DNA analysis first revealed--and subsequent cytogenetic analysis confirmed--that there was mosaic trisomy 14 in 5% of blood lymphocytes. There was normal (biparental) inheritance for chromosome 13, and there was no evidence of false paternity in genotypes of 11 highly polymorphic markers on human chromosome 21. Two cases of maternal UPD for chromosome 14 have previously been reported, one with a familial rob t(13;14) and the other with a t(14;14). There are several similarities among these patients, and a "maternal UPD chromosome 14 syndrome" is emerging; however, the contribution of the mosaic trisomy 14 to the phenotype cannot be evaluated. The study of de novo Robertsonian translocations of the type reported here should reveal both the extent of UPD in these events and the contribution of particular chromosomes involved in certain phenotypes.

Abnormalities, Multiple↗
PubMed2004

Analysis of chromosome segregation in sperm from a chromosome 2 inversion heterozygote and assessment of an interchromosomal effect.

Using fluorescence in situ hybridization (FISH) analysis, the chromosome segregation of a pericentric inversion of chromosome 2 was studied in spermatozoa. An interchromosomal effect (ICE) was also determined for chromosomes 13, 21, X, and Y. This chromosome inversion included more than 2/3 of the total length of the chromosome and the breaks points were in G-light bands. The frequency of non-recombinant sperm was 55.9%, and that of recombinant sperm was 34.5% (with a 1:1 ratio of duplication of the p arm and deletion of the q arm and vice versa). There was a significantly increased frequency of disomy for chromosome 2 (0.6%) compared to the other autosomes, suggesting that pairing and recombination of the inversion may predispose to nondisjunction. There was no significant difference between the frequencies of aneuploidy for chromosomes 13, 21, X, and Y for the chromosome inversion heterozygote compared to control donors. Thus we did not find evidence for an ICE.

Aneuploidy↗
PubMed1996

Human and porcine correspondence of chromosome segments using bidirectional chromosome painting.

The aim of this study was to determine the correspondence between human and porcine chromosome fragments using whole chromosome painting probes from both species in heterologous hybridization experiments (bidirectional heterologous chromosome painting). Bidirectional experiments allow the determination of segment-to-segment homologies between the chromosomes of these two species. Chromosome-specific painting probes from both species were, except one, obtained by DOP-PCR or PARM-PCR amplification of flow-sorted chromosomes. The probes labeled 95% of the total length of the porcine chromosomes with human painting probes and 60% of the human chromosomes in the reverse experiments. Syntenic relationships of chromosomal segments on the karyotype of both species were determined. There was close agreement between com- parative gene mapping data and the identified homologous segments; this comparison enabled orientation of the segments. We demonstrate that bidirectional heterologous chromosome painting is a highly efficient way of generating comparative cytogenetic maps.

Animals↗
PubMed1985

Organization and chromosomal specificity of autosomal homologs of human Y chromosome repeated DNA.

The human Y chromosome contains a group of repeated DNA elements, identified as 3.4-kilobase pair (kb) fragments in Hae III digests of male genomic DNA, which contain both Y-specific and non-Y-specific sequences. We have used these 3.4-kb Hae III Y fragments to explore the organizational properties and chromosomal distribution of the autosomal homologs of the non-Y-specific (NYS) 3.4-kb Hae III Y elements. Three distinct organizations, termed domains, have been identified and shown to have major concentrations on separate chromosomes. We have established that domain K is located on chromosome 15 and domain D on chromosome 16 and suggested that domain R is on chromosome 1. Our findings suggest that each domain is composed of a tandemly arrayed cluster of a regularly repeating unit containing two sets of repeated sequences: one that is homologous to the NYS 3.4-kb Hae III Y sequences and one that does not cross-react with the 3.4-kb Hae III Y repeats. Thus, these autosomal repeated DNA domains, like their Y chromosome counterparts, consist of a complex mixture of repeated DNA elements interspersed among each other in ways that lead to defined periodicities. Although each of the three identified autosomal domains cross-reacts with 3.4-kb Hae III Y fragments purified from genomic DNA, the length periodicities and sequence content of the autosomal domains are chromosome specific. The organizational properties and chromosomal distribution of these NYS 3.4-kb Hae III homologs seem inconsistent with stochastic mechanisms of sequence diffusion between chromosomes.

Animals↗
PubMed1988

Isolation of DNA sequences on human chromosome 21 by application of a recombination-based assay to DNA from flow-sorted chromosomes.

By merging two efficient technologies, bivariate flow sorting of human metaphase chromosomes and a recombination-based assay for sequence complexity, we isolated 28 cloned DNA segments homologous to loci on human chromosome 21. Subregional mapping of these DNA segments with a somatic cell hybrid panel showed that 26 of the 28 cloned DNA sequences are distributed along the long arm of chromosome 21, while the other 2 hybridize with sequences on the short arm of both chromosome 21 and other chromosomes. This new collection of probes homologous to chromosome 21 should facilitate molecular analyses of trisomy 21 by providing DNA probes for the linkage map of chromosome 21, for studies of nondisjunction, for chromosome walking in clinically relevant subregions of chromosome 21, and for the isolation of genes on chromosome 21 following the screening of cDNA libraries.

Animals↗
PubMed1991

Radiation-induced chromosomal breakage and rejoining in interphase-metaphase chromosomes of human lymphocytes.

The premature chromosome condensation (PCC) technique and conventional chromosome analysis were applied to examine the kinetics of radiation-induced primary chromosome breaks, their rejoining and formation of dicentrics in human peripheral blood lymphocytes (PBLs). Numbers of chromosomal elements and dicentrics per cell were analyzed for each dose. Dose-dependent increases were observed for chromosome fragments (linear) and dicentrics (linear/quadratic). For an assessment of repair kinetics, numbers of breaks and dicentrics were estimated immediately and at several recovery periods after irradiation, using the PCC technique. It was found that chromosome fragments restitute with time, whereas the dicentrics are formed very quickly and their frequency remains the same, despite the decline in the number of chromosome breaks at later recovery times. Fractionation experiments were conducted to study the time-dependent interaction of primary breaks in the formation of dicentric chromosomes. PBLs were irradiated with 3 Gy X-rays split into 2 equal fractions separated by different intervals up to 5 h. No marked difference was observed in the yield of dicentrics following the different fractionation protocols, except that the mean levels of dicentrics declined when the fraction interval was 4 h or more. It appears that most of the dicentrics are formed by misrepair of strand breaks, produced directly by radiation and not resulting from rejoining of existing breaks during the slow repair process which follows. We also studied the role of the chromatin configuration at the time of irradiation on the yield of chromosome fragments and dicentrics. Highly condensed chromatin due to pretreatment with 0.3 M NaCl was found to reduce the frequency of radiation-induced chromosomal aberrations.

Animals↗
PubMed1992

Gene amplification in a human osteosarcoma cell line results in the persistence of the original chromosome and the formation of translocation chromosomes.

Although gene amplification, a process that is markedly enhanced in tumor cells, has been studied in many different cell systems, there is still controversy about the mechanism(s) involved in this process. It is still unclear what happens to the DNA sequences that become amplified, whether they remain present at their original location (conservative gene amplification) or whether gene amplification necessarily results in a deletion at the original location (non-conservative gene amplification). We have studied gene amplification in a human osteosarcoma cell line, starting from a cell clone which contains only one copy of a plasmid integrate. Independent amplificants, originating from this clone and containing elevated plasmid copy numbers, were isolated and analyzed. Based on previous observations, encompassing the persistence of single-copy DNA sequences besides amplified DNA sequences clustered at a different location in the independent amplificants, we proposed an amplification pathway including a local duplication step and transposition of the duplicated DNA to other chromosomal positions. Now we have extended our study to more independent amplificants. We prove that the single-copy plasmid-containing chromosomes in the different amplificants and the single-copy plasmid-containing chromosome in the original parental cell clone are indeed identical, namely a translocation chromosome composed of at least three parts of which two originate from chromosomes 14 and 17. We show that the unit of amplification and the unit of the proposed transposition event are at least 1.5 Mb. We also demonstrate that the amplified DNA sequences, present at genomic locations other than the original single-copy DNA sequences, are preferentially associated with chromosome 16. We find that the amplified DNA sequences are often located at or near a site of chromosome translocation involving chromosome 16. In one cell clone we detect the amplified DNA sequences in most of the cells to be located within a complete chromosome 16 while in a minority of cells the amplified sequences are located at or near a breakpoint on a translocation chromosome 16. This indicates that this amplification region is highly unstable and frequently gives rise to translocation events.

Blotting, Southern↗
PubMed1993

Optical trapping for chromosome manipulation: a wavelength dependence of induced chromosome bridges.

Using a tunable titanium-sapphire laser, we have compared different wavelengths (from 700 to 840 nm) for their utility in optical trapping of chromosomes in mitotic rat kangaroo Potorous tridactylus (PtK2) cells. It was found that irradiation with a near-infrared light induces the sticking together of chromosome shoulders. The attached chromatids failed to separate, or separated with significant delay and formed a chromosome bridge during anaphase. Using this bridge (and induced c-mitosis) as a reference, we compared the action of different wavelengths (from 700 to 840 nm). Chromosomes were irradiated at metaphase and the cells were observed until the end of cytokinesis. Chromosomes were irradiated for different periods of time, using 130 mW of power at the objective focal plane. The biological responses observed after optical trapping were: (1) normal cell division, (2) formation of a temporary chromosome bridge, (3) formation of a permanent chromosome bridge, (4) complete blockage of chromosome separation (c-mitosis). The chromosomes were found to have a maximal sensitivity to 760-765 nm light and minimal sensitivity to 700 and 800-820 nm light. Cells with chromosomes irradiated for a long time, using wavelength 760-765 nm, generally were incapable of going through anaphase and remained in c-mitosis. We conclude that the optimal wavelengths for optical trapping are 700 and 800-820 nm.

Animals↗
PubMed2002

Topography of genetic elements of X-chromosome relative to the cell nucleus and to the chromosome X territory determined for human lymphocytes.

Topography of three genetic elements--dystrophin (dmd) exons 5-7 (E(1)), 46-47 (E(2)), and centromere of chromosome X (N(X)) were studied relative to cell nuclei and to chromosome X territories of spatially fixed human lymphocytes. Repeated three-dimensional (3D) dual color fluorescence in situ hybridization combined with high-resolution cytometry was used. In addition, the nuclear location of fluorescence weight centers (FWC), spatial volume, and maximal area per one section of chromosome-X territories were investigated. The larger (X(L)) and smaller (X(S)) homologous X-chromosomes were distinguished for each nucleus according to the 3D volume of their territories. The distributions of the [center of nucleus]-to-[genetic element] distances (radial distributions) of dmd exons E(1), E(2), centromere N(X) and FWC were very similar for both homologous X-chromosomes of female lymphocytes as well as for the chromosome X of the human male. On the other hand, larger average mutual distances between all pairs of signals (E(1), E(2), N(X), FWC) and larger average maximal area were observed for the larger chromosome (X(L)) in comparison with the smaller one (X(S)). The territory of the larger homologue showed also more irregular surface. The most significant differences between homologous X-chromosomes were found for N(X)-E(1), N(X)-E(2) and E(1)-E(2) distances that were in average about twice longer for X(L) as compared with X(S). These parameters correlate to each other and can be used for the reliable determination of more (de)condensed X-chromosome territory. The longer E(1)-E(2) distances for X(L) indicate more open chromatin structure of the dystrophin gene on this chromosome in contrary to closed structure on X(S). Substantially shorter distances of the dystrophin exons from the centromeric heterochromatin in X(S) as compared to X(L) can be explained by silencing effect of centromeres as described in Nature 1 (2000) 137.

Cell Nucleus↗
PubMed2003

Molecular characterization and chromosomal localization of two families of satellite DNA in Prochilodus lineatus (Pisces, Prochilodontidae), a species with B chromosomes.

Prochilodus lineatus, an abundant species in the Mogi-Guaçu river basin, represents a large part of the region's fishing potential. Karyotypic analyses based on classic cytogenetic techniques have revealed the presence of 54 meta-submetacentric type chromosomes, together with the occurrence of small supernumerary chromosomes with intra and interindividual variations. This paper describes the genomic organization of two families of satellite DNA in the P. lineatus genome. The chromosomal localization these two repetitive DNA families through fluorescence in situ hybridization (FISH) demonstrated that the SATH1 satellite DNA family, composed of approximately 900 bp, was located in the pericentromeric region of a group of chromosomes of the standard complement, as well as on all the B chromosomes. The SATH2 satellite family has a monomeric unit of 441 bp and was located in the pericentromeric regions of some chromosomes of the standard complement, but was absent in the B chromosomes. Double FISH analyses showed that these two families participate jointly in the pericentromeric organization of several chromosomes of this species. The data obtained in this study support the hypothesis that the B chromosomes derive from chromosomes of the standard complement, which are carriers of the SATH1 satellite DNA.

Animals↗
PubMed1987

125IdUrd-induced chromosome fragments, assayed by premature chromosome condensation, and DNA double-strand breaks have similar repair kinetics in G1-phase CHO-cells.

The effect of 125I-decay on cell lethality, and induction of chromosome and DNA damage, was studied in synchronous non-cycling, G1-phase CHO-cells. For this purpose a population of mitotic cells was allowed to divide and progress through S-phase in the presence of 125IdUrd. Cells were subsequently transferred to conditioned medium (C-med) obtained from plateau-phase cultures that allowed cells to divide and accumulate in G1-phase in a non-cycling state. To accumulate 125I-induced damage, cells were kept frozen at -80 degrees C. Freezing was carried out using a new method that optimally preserves cell integrity. After various times of cold storage, cells were thawed and assayed for survival, DNA and chromosome damage, either immediately or after various times in C-med. Neutral filter elution was used to assay repair of DNA double-strand breaks (dsbs), and premature chromosome condensation was used to assay repair of chromosome fragments and induction of ring chromosomes. The results indicate very little repair at the cell survival level (repair of PLD). At the DNA level an efficient repair of DNA dsbs was observed, with kinetics similar to those observed after exposure to X-rays. At the chromosome level a fast repair of prematurely condensed chromosome fragment was observed, with a concomitant increase in the number of ring chromosomes induced. The repair kinetics of chromosome fragments and DNA dsbs were very similar, suggesting that DNA dsbs may underlie chromosome fragmentation.

Animals↗
PubMed1990

Production and repair of chromosome damage in an X-ray sensitive CHO mutant visualized and analysed in interphase using the technique of premature chromosome condensation.

Production and repair of chromosome damage were studied in interphase xrs-5 cells by means of premature chromosome condensation (PCC). The results obtained were compared with those previously reported for CHO cells. Production of chromosome damage per unit of absorbed radiation dose was in xrs-5 cells larger by a factor of 2.6 than in CHO cells (5.2 breaks per cell per Gy). Changes in chromatin structure, associated with the radiation-sensitive phenotype of xrs-5 cells, that increase the probability of conversion of a DNA double-stand break (dsb) to a chromosome break are involved to explain this effect. Repair of chromosome breaks as measured in plateau-phase G1 cells was deficient in xrs-5 cells and the number of residual chromosome breaks was practically identical to the number of lethal lesions calculated from survival data. This observation suggests that non-repaired chromosome breaks are likely to be manifestations of lethal events in the cell. The yield of ring chromosomes scored after a few hours of repair was higher by a factor of three in xrs-5 compared with CHO cells. This increase in ring formation suggests an increase in the probability of misrepair of chromosome damage that may stem either from the reduced ability of xrs-5 cells to repair dsb, or from the higher production of chromosome fragments observed per cell and per Gy.

Animals↗
PubMed1997

Discordant phylogeographic patterns between the Y chromosome and mitochondrial DNA in the house mouse: selection on the Y chromosome?

We have compared patterns of geographic variation and molecular divergence of mitochondrial DNA (mtDNA) and Y chromosome over the range of the different subspecies of Mus musculus. MtDNA was typed for 305 nucleotides in the control region, the Y chromosome for 834 base pairs (bp) in Zfy introns and 242 bp in Sry, a Zfy2 18-bp deletion, and two microsatellites. Apparent discrepancies exist between the distributions of the lineages of mtDNA and of the two major Y-chromosome lineages thus defined: some subspecies share the same mtDNA lineage but have different Y-chromosome lineages or vice versa. One microsatellite reveals a geographically clustered variation inside the distribution of each Y-chromosome lineage, showing that new Y-chromosome variants can rapidly spread locally. The two major Y-chromosome lineages have a divergence time only about one fourth of that between mtDNA lineages. Although this recent coalescence of the Y chromosomes between subspecies could partly be due to a lower ancestral polymorphism of the Y chromosome, it suggests that secondary introgression after the radiation of the subspecies might have occurred. There is evidence that the differentiation of the Y-chromosome lineages contributes to partial reproductive isolation between subspecies, and patterns of molecular evolution suggest that selection has played a role in the rapid spread across subspecies.

Animals↗
PubMed1993

Interstitial localization of telomeric DNA sequences in the Indian muntjac chromosomes: further evidence for tandem chromosome fusions in the karyotypic evolution of the Asian muntjacs.

The Indian muntjac is believed to have the lowest chromosome number in mammals (2n = 6 in females and 2n = 7 in males). It has been suggested that a series of tandem chromosome fusions from an ancestral Chinese muntjac-like species (2n = 46) may have occurred during the karyotypic evolution of the Indian muntjac. In an earlier study, hybridization signals generated by the Chinese muntjac centromeric heterochromatin DNA probe (C5) were found to be distributed interstitially in the chromosomes of the Indian muntjac, providing supportive evidence for the tandem chromosome fusion theory. In this study, the highly conserved human telomeric DNA sequence (TTAGGG)n was localized by fluorescence in situ hybridization (FISH) on the metaphase chromosomes of three Cervidae species: the Indian muntjac, Chinese muntjac, and woodland caribou. As expected, hybridization signals were observed at the termini of almost every chromosome in all three species. In addition, interstitial hybridization signals were detected in chromosomes 1 and 2 of the Indian muntjac. The observed interstitial telomeric signals appeared to correspond to specific interstitial centromeric heterochromatin sites. These interstitial telomeric signals could represent remnant DNA sequences from the ancestral species telomeres, further supporting the tandem chromosome fusion theory. Furthermore, these observations permit the elucidation of the chromosome sites where breakage and fusion most likely occurred during the restructuring of the ancestral Chinese muntjac-like chromosomes to form the present day Indian muntjac karyotype.

Animals↗
PubMed1999

Chromosomes as well as chromosomal subdomains constitute distinct units in interphase nuclei.

Fluorescence in situ hybridization has demonstrated that chromosomes form individual territories in interphase nuclei. However, this technique is not suitable to determine whether territories are mutually exclusive or interwoven. This notion, however, is essential for understanding functional organizations in the cell nucleus. Here, we analyze boundary areas of individual chromosomes during interphase using a sensitive method based on replication labeling and immunocytochemistry. Thymidine analogues IdUrd and CldUrd were incorporated during S-phase into DNA of Chinese Hamster fibroblasts. Cells labeled with IdUrd were fused with cells labeled with CldUrd. Fused nuclei contained both IdUrd or CldUrd labeled chromosomes. Alternatively, the two labels were incorporated sequentially during successive S-phases and segregated to separate chromosomes by culturing the cells one more cell cycle. Metaphase spreads showed IdUrd-, CldUrd- and unlabeled chromosomes. Some chromatids were divided sharply in differently labeled subdomains by sister chromatid exchanges. With both methods, confocal imaging of interphase nuclei revealed labeled chromosomal domains containing fiber-like structures and unlabeled areas. At various sites, fiber-like structures were embedded in other territories. Even so, essentially no overlap between chromosome territories or between subdomains within a chromosome was observed. These observations indicate that chromosome territories and chromosomal subdomains in G(1)-phase are mutually exclusive at the resolution of the light microscope.

Animals↗