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PubMed1984

DNA sequences and chromosome structure.

In this review evidence for the possible relationship between higher order chromosome structure and the distribution of tandem and dispersed repeated sequences in DNA has been examined. Evidence from studies of chromosome diminution in lower eukaryotes suggests that simple sequence DNAs may have a germ-line function and, in mammals, changes in simple sequence methylation, associated with changes in chromosome condensation, support the idea that the centromeric and telomeric heterochromatin may have a function in germ-line cells. For the major families of dispersed repeats, the weight of available evidence suggests that if they do play a role in chromosome organization, it is not an important one. Cytosine methylation is suggested as a candidate for a role in organizing the chromatin. Long-range patterns of methylation in vertebrates, the relationship of this to gene structure, and the association of changes in methylation with gene activity accord with current evidence linking specific nuclear structures to defined points in coding regions.

Chromosomes↗
PubMed1981

Chromosome structure and mitosis in the dinoflagellates: an ultrastructural approach to an evolutionary problem.

Chromosome structure and mitosis have been examined in three evolutionarily diverse members of the Pyrrophyta. Chromosome uncoiling, revealing the chromonema, has been correlated with the uptake of [3H]thymidine. In addition, chromosome uncoiling has been observed during gamete formation, gamete fusion, and in the nucleolar organizing region of the chromosomes suggesting that dinoflagellate chromosomes undergoing duplication, transcription or pairing have a morphology different from the characteristic tightly banded structure generally observed during most of interphase and mitosis. The dinoflagellate chromonema is composed of 2.5-nm fibers and 9.0-nm granules coiled into a helix around a central core of 9.0-nm fibers. Chromosome attachment to nuclear channels and kinetochore division and separation have been examined in several dinoflagellates. After evaluating many nuclear and cytoplasmic characteristics of the dinoflagellates it appears that this group of organisms are true eukaryotes which may be on the main line to the evolution of the mitotic spindle typical of higher plant and animals cells.U

Animals↗
PubMed1999

Chromosomal structures of bottom fermenting yeasts.

A genomic comparison of bottom fermenting yeasts was performed by pulsed-field gel electrophoresis and Southern blot analysis with some S. cerevisiae gene probes. We confirmed that strains of bottom fermenting yeast have four chromosomes originating from S. bayanus. Since the structures of these chromosomes were recombined with S. cerevisiae chromosomes, these S. bayanus chromosomes could be differentiated from S. cerevisiae chromosomes using Southern hybridization. Our Southern hybridization results indicate that bottom fermenting yeasts have both chromosomes originating from both S. cerevisiae and S. bayanus. It was reconfirmed that top fermenting yeast should be classified as S. cerevisiae, based on the chromosomal structure. The chromosomal structure of S. pastorianus CBS1538, the type stain of S. pastorianus, was also investigated. This strain has chromosomes originating only from S. bayanus. S. carlsbergensis CBS1513 has chromosomes originating from both S. cerevisiae and S. bayanus. From these results, we contend that bottom fermenting yeasts should be classified as S. carlsbergensis.

Blotting, Southern↗
PubMed2004

Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy.

Acetic acid treatment has been frequently used to remove cellular contaminants from plant chromosome samples for structural analyses by scanning electron microscopy and atomic force microscopy (AFM). We evaluated the effects of various concentrations of acetic acid treatments on barley chromosome structures by using AFM. The long-term 45% acetic acid treatment significantly damaged the chromosome structures, although the treatment effectively removed the cellular contaminants. On the other hand, the treatment with 15% acetic acid could not obtain sufficiently clean chromosome samples and the chromosome surface structures could not be observed. In contrast, we obtained clean chromosome preparation without severe damage by using an intermediate concentration (30%) of acetic acid treatment. In the centromeric region, we could observe fiber structures with a width of 100 nm, which were composed of ca. 50-nm granules and aligned to the axes of chromosomes. Thus, AFM analysis of chromosomes appropriately treated with acetic acid will provide important insights into the organization of higher-order structures of plant chromosomes.

Acetic Acid↗
PubMed1994

Identification of chromosomal structural alterations in human ovarian carcinoma cells using combined GTG-banding and repetitive fluorescence in situ hybridization (FISH).

In order to identify chromosomal structural alterations in the ovarian carcinoma cell line MLS/P, fluorescence in situ hybridization with centromeric probes for chromosomes 1, 8, 9, 13/21, 14/22, 15, 17, and X and whole chromosome painting probes for chromosomes 1, 3, 4, 5, 7, 8, 9, 10, 12, 13, 14, 17, 19, 22, and X were performed subsequent to GTG-banding. This combined approach identified 14 of the 18 clonal structurally rearranged chromosomes, with the X chromosome involved in three aberrations. In contrast, only eight of the 14 rearrangements were identifiable by G-banding alone. These results indicate that the combined G-banding and FISH approach can significantly improve the cytogenetic analysis of human neoplasia.

Azure Stains↗
PubMed1994

Genomic stability and instability in different neuroepithelial tumors. A role for chromosome structure?

Selected childhood and adult neoplasm exemplify fundamental differences in their propensity for genomic change. DNA replication is essential for the formation of neuroepithelial tumors, probably because the genome can be remodeled. Nonetheless, several differentiated and stable childhood neoplasms retain their nuclear controls for differentiation. In contrast, rapidly arising gliomas often show a variety of phenotypic changes. Genomic plasticity and instability allow gliomas to flexibly adapt to new environments. Gene changes (in DNA) can be limited in childhood tumors whereas more widespread genetic changes in malignant gliomas indicate a fundamental alteration in many chromosome regions. Can such regions be defined? We used one repeated DNA sequence (TTAGGG)n, present at the end of all normal human chromosomes, to investigate chromosome termini in more detail. Pulsed-field gel electrophoresis showed this region can be unusually variable, as several other multilocus probes did not reveal comparable changes. Because telomeres form unique chromosomal structures, and are thought to provide essential signals to position chromosomes in the interphase nucleus, it was pertinent to assess these regions by in situ hybridization. Many telomeric domains localized at variable as well as interior nuclear positions in glioma cells. These positions, which are presumably abnormal, may be generated by the DNA variants observed. Such position changes may contribute to the more general 'disorder' observed in glioma nuclei. Other chromosome domains with a unique DNA-protein structure may define additional genomic loci that are preferentially modified in neoplasia. A fundamental understanding of chromosome structure should clarify the problem of multilocus instability in glioblastoma.

Age of Onset↗
PubMed2003

On-substrate lysis treatment combined with scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes.

The proper function of the genome largely depends on the higher-order architecture of the chromosome. To understand the detailed chromosome structure in a native state, we developed an on-substrate procedure of subcellular fractionation suitable for the observation by atomic force microscopy (AFM). HeLa cells on a coverslip were successively treated with a detergent and a high-salt solution to remove the cytoplasmic and nucleoplasmic materials. A closer observation of the nucleus by AFM revealed that the interphase chromosome is composed of a granular unit of approximately 80 nm in diameter. Subsequent mild treatment with deoxyribonuclease I (10 U ml(-1)) exposed these units more clearly, which enabled us to uncover the 80-nm granules forming a fibre of approximately 80 nm width. In the cytoplasmic regions, cytoskeletal fibres with varying widths (10-70 nm) were observed. These observations suggest that the 80 nm granular fibre is a fundamental structural unit of the interphase chromosome. This on-substrate procedure was also applied to Escherichia coli. Cells attached on a coverslip were successively treated with lysozyme and detergent to partially release the nucleoid onto the substrate. The AFM observation revealed that the approximately 80 nm fundamental structural unit forms a granular fibre similar to that of HeLa cells. These results suggest that the fundamental mechanism of chromosome packing is common in both prokaryotes and eukaryotes.

Cell Nucleus Structures↗
PubMed1990

Clonal structural chromosomal rearrangements in lymphocytes of four patients with Werner's syndrome.

Multiple numerical and structural chromosome abnormalities were found in cultured lymphocytes of four patients with Werner's syndrome. The proportion of metaphases with structural and/or numerical aberrations varied from 30 to 44% and several of them were clonal. These results confirm definitively that Werner's syndrome is a chromosome rearrangement syndrome and that these non-constitutional chromosome changes are not exclusive of cultured fibroblasts but present also in lymphocytes.

Adult↗
PubMedDate not supplied

[Rejoining pathways underlying intrachange formation depend on interphase chromosome structure].

Fluorescence in situ hybridization technique with dual-arm painting of the same chromosome allows to study radiation induced intrachromosomal exchange aberrations (intrachanges). The formal method for analysis of FISH data developed by Savage and Simpson includes an arrangement of chromosomal reactive breaks on chromosomes and chromosome arms (CAB system). That method predicts types and frequencies of aberrations assuming random restitution/rejoining of breaks free ends. However experimental data suggest that many aberrations are formed non-uniformly along the chromosomes and chromosome arms. In the present paper the system for classifying rejoining pathways underlying intrachange formation is proposed which does not require random restitution/rejoining suggestion. It takes into account the parameters of interphase chromosome structure. Types and frequencies of intrachanges are considered by exploring different hypotheses about exchange initiating chromosomal lesions.

Chromosome Aberrations↗
PubMedDate not supplied

Novel recurrent structural chromosomal aberrations in primary bladder cancer.

BACKGROUND: Bladder cancer is a heterogeneous genetic disease and, to date, no specific cytogenetic abnormality has been established. The detection of recurrent genetic changes with common breakpoints is of special interest, facilitating the identification of genes implicated in carcinogenesis. The aim of this study was to investigate recurrent structural chromosomal aberrations with common breakpoints and to correlate them with the histological stage of tumors. MATERIALS AND METHODS: Fifteen patients with transitional cell carcinoma of the bladder were cytogenetically studied by direct culture of primary tumor cells and G-banding technique. RESULTS: Most of the cases studied exhibited very complex karyotypes. Recurrent structural aberrations were observed involving, according to frequency, chromosomal regions 11p15, 3p12, 14q32, 19q13 and 6q23. Isochromosomes i(8q), i(17q) and i(6p) were also observed. CONCLUSION: Conventional cytogenetics continues to be valuable in cancer study, detecting common chromosomal breakpoints. Of interest was the detection of novel recurrent structural chromosomal aberrations including involvement of 11p15, 14q32 and 19q13, while a correlation of recurrent abnormalities observed with tumor stage was also evaluated.

Carcinoma, Transitional Cell↗
PubMed1997

Primed in situ (PRINS) labeling for rapid detection of numeric and structural chromosome anomalies.

Primed in situ (PRINS) labeling has been applied to replace the traditional fluorescence in situ hybridization (FISH) method for the detection of specific sequences in situ in several numerical and structural chromosome anomalies. PRINS is based on sequence-specific annealing in situ of an unlabeled DNA probe or oligonucleotide primer. The probe serves as a primer for chain elongation in situ, using the labeled nucleotides as substrate. An oligonucleotide, (CCCTAA) representing human telomeric sequences, was mixed with nucleotides, biotin-16-dUTP, and Taq DNA polymerase, and applied on metaphase slides with ring chromosomes 4, 13, 18, X and Y. Primers for alpha-satellite sequences specific for the centromeric regions of human chromosomes 13, 15, 18, X and Y were also used to characterize the nature and origin of unidentifiable supernumerary marker chromosomes. The specificity of PRINS in differentiating centromeric sequences of chromosome [3 from 21 which is not possible with FISH, was demonstrated. Absence of the telomeric sequences in all of the ring chromosomes was noted in normal and abnormal phenotypes. The results suggest a mechanism of ring formation, an end-to-end fusion after loss of the palindromic nucleotide sequences at the telomeres PRINS, a fast and sensitive method of detecting nucleic acid sequences in situ, may be a reliable technique for detecting chromosomal aneuploidies and some structural rearrangements.

Chromosome Aberrations↗
PubMed2000

A cruciform structural transition provides a molecular switch for chromosome structure and dynamics.

The interaction between specific sites along a DNA molecule is often crucial for the regulation of genetic processes. However, mechanisms regulating the interaction of specific sites are unknown. We have used atomic force microscopy to demonstrate that the structural transition between cruciform conformations can act as a molecular switch to facilitate or prevent communication between distant regions in DNA. Cruciform structures exist in vivo and they are critically involved in the initiation of replication and the regulation of gene expression in different organisms. Therefore, structural transitions of the cruciform may play a key role in these processes.

Base Pairing↗
PubMed1990

Congenital cardiovascular malformations (CCVM) and structural chromosome abnormalities: a report of 9 cases and literature review.

Nine cases of congenital cardiovascular malformations (CCVM) with associated unbalanced structural chromosomal abnormalities were ascertained in a population-based study of heart defects, constituting 0.4% of the 2,103 cases of CCVM in the Baltimore-Washington Infant Study (BWIS). This represents a four-fold increase over the general population rate. In an effort to determine possible phenotype/karyotype correlations, the literature was searched for cases with similar karyotypic abnormalities. This comparison of 223 literature cases of karyotypic abnormalities with nine similar cases ascertained by heart malformation has provided the opportunity to review cardiac defects reported in cases of structural abnormalities of chromosomes 1, 3, 7, 8, 9, 10, 11, 15, and 18. The most common cardiac malformation present in the chromosomal cases was ventricular septal defect (VSD) (39%); similarly VSD is the most common CCVM among children with heart defects, although it is the primary defect in only 20% of the BWIS cases. Among all heart defects in the BWIS, atrial septal defect (ASD) represents 5.5% of all cases, but in cases of 8p duplication, ASD is present in 41%. In addition, 40% of cases of 9p duplication had an ASD. Similarly, 35% of cases of 11q duplication had an ASD. While the suggestion of specific karyotype/phenotype association is premature, information on additional cases might clarify the possibility that genetic determinants related to septum formation may reside on chromosome 8, 9, and/or 11. The variety of chromosomal abnormalities in cases with ventricular septal defect indicates one type of genetic heterogeneity that may be involved in this very common heart defect.

Case-Control Studies↗
PubMed1983

Rates of mutant structural chromosome rearrangements in human fetuses: data from prenatal cytogenetic studies and associations with maternal age and parental mutagen exposure.

In 27,225 prenatal cytogenetic studies of amniotic fluid reported to the New York State Chromosome Registry and the United States Interregional Chromosome Register System, there were 61 cases with a structural chromosomal abnormality not known inherited, a rate per 1,000 of 2.24. Of these 33, 1.21 per 1,000 were known de novo and nonmosaic; consequently, the rate of events resulting from germinal mutation is highly likely to be between these two limits. The rates per 1,000 of unbalanced abnormalities were 0.59-1.29; of balanced abnormalities, 0.62-0.96; of balanced Robertsonian translocations, 0.22-0.29; and of unbalanced Robertsonian translocations, 0.07-0.11. The rates of fetuses with supernumerary markers and fragments were unexpectedly high: 0.26-0.70 per 1,000. These abnormalities were associated with increased maternal age (38.0 +/- 5.4 to 38.4 +/- 3.6 compared to 35.6 +/- 4.3 in controls), but even after adjustment for the bias to preferential study of older women, the observed rates of these supernumerary abnormalities were greater than would be expected from live-birth studies or rates estimated in all recognized conceptuses. There were trends to elevated maternal age for the group of all balanced rearrangements, and to diminished maternal age for the nonsupernumerary, non-Robertsonian unbalanced rearrangements. In 136 women studied primarily because of exposure to a putative mutagen, a de novo deletion and an inversion not known inherited were detected. The rate of abnormality in these 136, 1.47%, was significantly greater than the rate of abnormality in the remainder: 0.14%-0.22%.

Adult↗