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PubMed2001

Loss of the Y chromosome is a frequent chromosomal imbalance in pancreatic cancer and allows differentiation to chronic pancreatitis.

In a study for the identification of genomic alterations in pancreatic cancer, representational difference analysis was used and led to the isolation of 2 distinct fragments, deleted on the Y chromosome in the xenografted tumor DNA of a male patient with an adenocarcinoma of the pancreas. Loss of Y chromosomal material was further studied in 11 pancreatic cancer cell lines of male origin, using PCR amplification of 5 sequence tagged sites (STSs) distributed along the Y chromosome; 8/11 cell lines exhibited a complete loss of the Y chromosome and 3 had deletions. To examine the status of the Y chromosome in situ, interphase FISH analysis was performed on paraffin sections from pancreatic carcinoma (n=7) and chronic pancreatitis (n=7) tissues, and the loss of Y-chromosomal STS-markers was studied in 6 xenograft tumors obtained from male pancreatic cancer patients. This analysis revealed that a loss of the Y chromosome occurs in vivo in primary pancreatic tumor cells, whereas the Y chromosome was intact in chronic pancreatitis. Our data suggest that loss of Y is a frequent event occurring in male pancreatic tumors. Although there is no evidence for a functional implication of Y chromosome loss, it effectively differentiates between a malignant and a benign condition as e.g. chronic pancreatitis. Thus, this genetic alteration may be of diagnostic use.

Animals↗
PubMed2005

The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence.

To catalog data on chromosomal aberrations in cancer derived from emerging molecular cytogenetic techniques and to integrate these data with genome maps, we have established two resources, the NCI and NCBI SKY/M-FISH & CGH Database and the Cancer Chromosomes database. The goal of the former is to allow investigators to submit and analyze clinical and research cytogenetic data. It contains a karyotype parser tool, which automatically converts the ISCN short-form karyotype into an internal representation displayed in detailed form and as a colored ideogram with band overlay, and also has a tool to compare CGH profiles from multiple cases. The Cancer Chromosomes database integrates the SKY/M-FISH & CGH Database with the Mitelman Database of Chromosome Aberrations in Cancer and the Recurrent Chromosome Aberrations in Cancer database. These three datasets can now be searched seamlessly by use of the Entrez search and retrieval system for chromosome aberrations, clinical data, and reference citations. Common diagnoses, anatomic sites, chromosome breakpoints, junctions, numerical and structural abnormalities, and bands gained and lost among selected cases can be compared by use of the "similarity" report. Because the model used for CGH data is a subset of the karyotype data, it is now possible to examine the similarities between CGH results and karyotypes directly. All chromosomal bands are directly linked to the Entrez Map Viewer database, providing integration of cytogenetic data with the sequence assembly. These resources, developed as a part of the Cancer Chromosome Aberration Project (CCAP) initiative, aid the search for new cancer-associated genes and foster insights into the causes and consequences of genetic alterations in cancer.

Base Sequence↗
PubMed1992

Characterization of a complex chromosomal rearrangement maps the locus for in vitro complementation of xeroderma pigmentosum group D to human chromosome band 19q13.

Microcell-mediated chromosome transfer (MMCT) is a powerful genetic technique that permits the transfer of a single chromosome from one mammalian cell to another. The utility of MMCT for gene mapping strategies is critically dependent on the careful characterization of the chromosomes being transferred. We have recently reported the identification of a single rearranged human chromosome, designated Tneo, which corrects the UV sensitivity and excision repair defect of cells of xeroderma pigmentosum genetic complementation group D (XP-D) in culture (Flejter WL et al., Proc Natl Acad Sci USA 89:261-265, 1992). Additionally, those studies demonstrated a role for the excision repair cross-complementing 2 (ERCC2) gene in the observed phenotypic correction. We now report the results of detailed conventional and molecular cytogenetic characterization of the complementing Tneo chromosome. This analysis revealed a complex rearrangement involving material from human chromosomes 16, 17, and 19. Characterization of deletions of Tneo which retained or lost XP-D complementing ability mapped the gene responsible for phenotypic correction to a small region of the terminal q-arm of this chromosome. This region includes the previously described human DNA repair gene cluster located in the region 19q13.2-q13.3, a result consistent with the notion that the in vitro correction of XP-D cells by the Tneo chromosome is rendered by the ERCC2 locus. The data illustrate the potential value of detailed cytogenetic characterization of a human chromosome present in a somatic cell hybrid, even when that material involves complex rearrangements.

Cell Line↗
PubMed1987

(dC-dA)n.(dG-dT)n sequences have evolutionarily conserved chromosomal locations in Drosophila with implications for roles in chromosome structure and function.

In situ hybridization of (dC-dA)n.(dG-dT)n to the polytene chromosomes of Drosophila melanogaster reveals a clearly non-random distribution of chromosomal sites for this sequence. Sites are distributed over most euchromatic regions but the density of sites along the X chromosome is significantly higher than the density over the autosomes. All autosomes show approximately equal levels of hybridization except chromosome 4 which has no detectable stretches of (dC-dA)n.(dG-dT)n. Another striking feature is the lack of hybridization of the beta-heterochromatin of the chromocenter. The specific sites are conserved between different strains of D. melanogaster. The same overall chromosomal pattern of hybridization is seen for the other Drosophila species studied, including D. simulans, a sibling species with a much lower content of middle repetitive DNA, and D. virilis, a distantly related species. The evolutionary conservation of the distribution of (dC-dA)n.(dG-dT)n suggests that these sequences are of functional importance. The distribution patterns seen for D. pseudoobscura and D. miranda raise interesting speculations about function. In these species a chromosome equivalent to an autosomal arm of D. melanogaster has been translocated onto the X chromosome and acquired dosage compensation. In each species the new arm of the X also has a higher density of (dC-dA)n.(dG-dT)n similar to that seen on other X chromosomes. In addition to correlations with dosage compensation, the depletion of (dC-dA)n.(dG-dT)n in beta-heterochromatin and chromosome 4 may also be related to the fact that these regions do not normally undergo meiotic recombination.

Animals↗
PubMed1994

Rapid generation of whole chromosome painting probes (WCPs) by chromosome microdissection.

A strategy for rapid construction of whole chromosome painting probes (WCPs) by chromosome microdissection has recently been developed. WCPs were prepared from 20 copies of each target chromosome microdissected from normal human metaphase chromosomes and then directly amplified by PCR using a universal primer. Fifteen WCPs, including chromosomes 1, 3, 6, 7, 9, 12, 13, 14, 15, 17, 19, 20, 21, 22, and X, have been generated using this strategy. The probe complexity and hybridization specificity of these WCPs have been characterized by gel electrophoresis and fluorescence in situ hybridization. Analysis of WCPs constructed by chromosome microdissection indicated that microdissected WCPs invariably provide strong and uniform signal intensity with no cytologically apparent cross-hybridization. To demonstrate the application of WCPs generated from microdissection, we have used these probes to detect complex chromosome rearrangements in a melanoma cell line, UM93-007. Two different translocations involving three chromosomes [t(1;3;13) and t(1;7;13)] have been identified, both of which were undetectable by conventional banding analysis. Further application of these WCPs (including generation of WCPs from mouse and other species) should greatly facilitate the cytogenetic analysis of complex chromosome rearrangements.

Animals↗
PubMed1995

Molecular characterization of tiny ring X chromosomes from females with functional X chromosome disomy and lack of cis X inactivation.

Small ring X chromosomes were first described in mosaic karyotypes of females with the relatively benign phenotype of Turner syndrome. The presence of these rings in association with more severe phenotypes including mental retardation has raised the possibility that they lack sequences necessary for X chromosome inactivation, specifically genes within the X inactivation center (XIC) essential for cis X-inactivation. We recently showed that ring X chromosomes ascertained because of the severe phenotype do not express XIST, a candidate for the relevant gene, and that they are in fact active chromosomes. We now report studies of the genetic content of 11 of these ring X chromosomes (9 associated with severe phenotypes). Our results indicate that these chromosomes contain contiguous segments of DNA and have variable proximal and distal breakpoints and some include mainly long arm or mainly short arm sequences. As expected for ring chromosomes, they lack telomeric sequences. Many of the ring chromosomes lack the XIST locus, consistent with XIST being necessary for cis inactivation. However, the breakpoints in four ring chromosomes that have XIST sequences but do not express XIST suggest that other sequences within the XIC distal to XIST as it is now defined are also needed.

Animals↗
PubMed1997

Physical and linkage mapping of human chromosome 17 loci to dog chromosomes 9 and 5.

Genome mapping in the dog is in its early stages. Here we illustrate an approach to combined physical and linkage mapping of type 1 anchor (gene) loci in the dog using information on syntenic homology from human and mouse, an interbreed cross/backcross, and a strategy for isolation of dog genomic clones containing both gene-specific sequences and simple sequence repeat polymorphisms. Eleven gene loci from human chromosome 17q (HSA17q) were mapped to the centromeric two-thirds of dog chromosome 9 (CFA9), an acrocentric chromosome of medium size: P4HB, GALK1, TK1, GH1, MYL4, BRCA1, RARA, THRA1, MPO, NF1, and CRYBA1. Eight of these were also positioned on a linkage map spanning 38.6 cM. Based on combined fluorescence in situ hybridization and linkage mapping, the gene order on CFA9 is similar to that of the homologous genes on HSA17q and mouse chromosome 11 (MMU11), but in the dog the gene order is inverted with respect to the centromere. Canine loci, GALK1, TK1, GH1, MYL4, THRA1, and RARA constitute a closely linked group near the centromeric end of CFA9, spanning a genetic distance of only 4.7 cM. Canine NF1 and CRYBA1 lie distally, near the lower border of the Giemsa band adjacent to the distal one-third of CFA9. NF1 and CRYBA1 are loosely linked to the more centromeric group (31.2 cM). No HSA17 genes were found on the telomeric one-third of CFA9. Painting of dog chromosomes with a human whole chromosome 17 probe showed hybridization with only the proximal two-thirds of CFA9, consistent with the conclusion that the distal one-third corresponds to a segment or segments of other human chromosomes. Two loci, GLUT4 and PMP22, located on HSA17p, were mapped by FISH to dog chromosome 5 in a region also identified by the whole human chromosome 17 paint, indicating disruption of HSA17 syntenic homology at the centromere.

Animals↗
PubMed1982

Assigning the polymorphic human insulin gene to the short arm of chromosome 11 by chromosome sorting.

We have determined the subchromosomal location of the human insulin gene by analyzing DNA isolated from sorted human metaphase chromosomes. Metaphase chromosome suspensions were sorted into fractions according to relative Hoechst fluorescence intensity by the fluorescence activated chromosome sorter. The chromosomal DNA in each fraction was characterized by restriction endonuclease analysis. Initial sorts indicated that the insulin gene-containing fragment resided in a fraction containing chromosomes 9, 10, 11, and 12. Studies of cell lines that contained chromosome translocations permitted the assignment of the insulin gene to a derivative chromosome that contains portions of the short arm of chromosome II. Simultaneous sorting of the normal homolog from this small derivative chromosome separated the two different sized insulin gene-containing restriction fragments in this individual. These data indicate that the two restriction fragments represent insulin gene polymorphism and not duplicate gene loci.

Alleles↗
PubMed1981

Protein-depleted chromosomes. II. Experiments concerning the reality of chromosome scaffolds.

Chromosome scaffolds are chromosome-shaped bodies, composed of non-histone proteins, which remain when the histones are extracted from chromosomes. Because of the well-known tendency of chromosomal proteins to aggregate, we have tested the possibility that chromosome scaffolds might be produced by aggregation of proteins during the preparation of scaffolds. Extraction of histones in the presence of sucrose, which inhibits aggregation, results in a much looser structure lacking the characteristic appearance of a scaffold, although sucrose does not extract any extra proteins. Extraction of histones from chromosomes in situ on EM grids produced only a network of fine fibres without a scaffold-like structure, while digestion of DNA from typical chromosome scaffolds in situ fell only discrete particles of protein and not a continuous structure. We conclude, therefore, that the typical appearance of chromosome scaffolds produced by histone extraction may well represent an artefact resulting from protein aggregation. Our experiments suggest further that DNA, as well as protein, is a structural component of whatever type of core structure is responsible for maintaining the form of chromosome.

Animals↗
PubMed1978

Three chromosomes' (7;9;22) rearrangement and the origin of the Philadelphia chromosome.

A woman with chronic myelocytic leukemia had the Philadelphia chromosome and a complex four-break--three-chromosome rearrangement. The q32 leads to q34 portion of chromosome 9 is translocated to band q22 of chromosome 7, and at the end of this segment is attached the deleted q11 leads to qter portion of chromosome 22. A review of 12 cases of the Philadelphia chromosome originating by the rearrangement of three or more chromosomes reveals that chromosomes 9 and 22 are always involved, while the third chromosome is a different one in each case. We discuss the hypothesis that the 22q segment is always specifically attached to band 9q34 wherever this portion of 9q is transposed.

Aged↗
PubMed1994

The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary.

Fluorescence in situ hybridization (FISH) of microlibraries established from distinct chromosome subregions can test the evolutionary conservation of chromosome bands as well as chromosomal rearrangements that occurred during primate evolution and will help to clarify phylogenetic relationships. We used a DNA library established by microdissection and microcloning from the entire long arm of human chromosome 2 for fluorescence in situ hybridization and comparative mapping of the chromosomes of human, great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus) and Old World monkeys (Macaca fuscata and Cercopithecus aethiops). Inversions were found in the pericentric region of the primate chromosome 2p homologs in great apes, and the hybridization pattern demonstrates the known phylogenetically derived telomere fusion in the line that leads to human chromosome 2. The hybridization of the 2q microlibrary to chromosomes of Old World monkeys gave a different pattern from that in the gorilla and the orang-utan, but a pattern similar to that of chimpanzees. This suggests convergence of chromosomal rearrangements in different phylogenetic lines.

Animals↗
PubMed2002

Origin of an apparent B chromosome by mutation, chromosome fragmentation and specific DNA sequence amplification.

The present study documents the de novo origin of an apparent B chromosome in Plantago lagopus. The origin was associated with mutation (aneuploidy), chromosome fragmentation, specific DNA sequence amplification, addition of telomeric repeats, and centromeric misdivision. It originated in the progeny of trisome 2, from the excision of 5S rDNA and 18S, 5.8S, 25S rDNA sequences located on chromosome 2, and within a few generations acquired many characteristics of an apparent B chromosome. The B chromosome has preferential transmission through the male (41%, P<0.025) and female gametes (42%, P<0.01) but does not affect plant phenotype. The B chromosome is completely heterochromatic, has a functional centromere and does not pair at meiosis with any A chromosomes of the standard complement. Fluorescence in situ hybridization analysis showed that it arose from massive amplification of 5S rDNA sequences, has 18S, 5.8S, 25S rDNA sequences at the ends of both arms and telomeric repeats at both termini. Ag-NOR-banding and determination of the maximum number of nucleoli in interphase cells indicate that the nucleolar organizer regions at the ends of both arms of the B chromosome are active in organizing nucleoli. RNA blot analysis showed that the 5S rDNA sequences are not transcribed. To our knowledge, this is the first report that fully documents one of the mechanisms by which B chromosomes may arise in nature.

Base Sequence↗
PubMed1981

Chromosome alteration and the development of tumors. XXIII. Banding karyotype analyses of methylcholanthrene-induced tumors in the Indian spiny mouse, Mus platythrix, with special regard to the anomalies of chromosomes with nucleolar organizer regions.

In the Indian spiny mouse, Mus platythrix (2n = 26), six tumors were induced by 3-methylcholanthrene, and their karyotypes were analyzed in the primary state by G-banding. The chromosome numbers of these tumors were widely distributed ranging from diploid to tetraploid, but the frequency of cells exhibiting diploidy was the highest. Among these cells, the frequency of the cells with a normal diploid karyotype was only 27%, but the remaining cells (73%) showed pseudo- or near-diploid karyotypes. Although several numerical and structural anomalies of the chromosomes were observed in these tumor cells, centric fusion and translocation was most commonly seen, and that of trisomy and monosomy ranked second. Among 13 chromosome pairs, higher frequencies of chromosome anomalies were observed in the chromosomes No. 5, 8, and 12. Anomalies of the other autosomes were related primarily to centric fusion with chromosomes No, 5, 8, or 12, those of the X chromosome were mainly numerical changes. Taking into account the nucleolar organizer regions (NORs), which always occurred in chromosome pairs No. 5, 8 and 12 in this species, a possible relationship between the anomalies of those chromosomes containing NORs and the malignant transformation of cells is proposed.

Animals↗
PubMed1987

Nonrandom chromosomal aberrations and clonal chromosomal evolution in acute leukemia associated with Down's syndrome.

Nine Down's syndrome (DS) children, four with acute leukemia, one with acute leukemia as well as rhabdomyosarcoma, and four with other hematologic disorders, were analyzed for constitutional and acquired chromosomal aberrations. Acquired clonal chromosomal aberrations were identified only in the acute leukemia cases, and four of the five acute leukemia demonstrated numerical and/or structural aberrations involving chromosomes #8, #19, and #21. Of the 11 aneuploid stem cell lines identified in the five acute leukemia cases, trisomy 21, trisomy 8, trisomy 19, and tetrasomy or pentasomy 21 was found in 11, seven, four, and two lines, respectively. The frequent appearance of multiple stem cell lines with common and/or overlapping chromosomal aberrations in acute leukemia cases demonstrates the existence of genomic instability and heterogeneity of the neoplastic cell population, which results from clonal chromosomal evolution. Furthermore, trisomy 19 was identified only with the concurrent presence of trisomy 8, suggesting that the nondisjunction of chromosome #19 probably occurred after that of #8. Trisomy 21 was observed in every aneuploid stem cell line and, in one case, trisomy 21 was maintained in the bone marrow leukemic cells but not in the orbital rhabdomyosarcoma cells, indicating that this constitutional chromosomal aberration is probably crucial for and predisposed to the development of acute leukemia in DS patients. The association of acquired clonal chromosomal aberrations, especially those involving chromosomes #8, #19, and #21, with DS acute leukemia strongly suggests the clinical implication of cytogenetic analysis in the diagnosis of acute leukemia development in DS patients.

Acute Disease↗
PubMed2003

The cell biology of a novel chromosomal RNA: chromosome painting by XIST/Xist RNA initiates a remodeling cascade.

X chromosome inactivation begins when a novel chromosomal RNA (cRNA) from the imprinted mouse Xist or human XIST locus coats or "paints" one X chromosome in cis and initiates a cascade of chromosome remodeling events. Molecular cytological studies have proven invaluable for understanding the distinctive cellular behavior of this singular RNA involved in chromosome structure and regulation. While the detailed mechanism of XIST/Xist (X-inactivation Specific Transcript) RNA function remains largely unknown, recent advances provide new insights into the complex cellular factors which impact the RNA's localization to the chromosome, as well as the early events of chromosome remodeling that follow painting by Xist RNA. Because chromatin changes can be directly visualized on a silenced chromosome, X chromosome inactivation provides an advantageous model to investigate genome-wide heterochromatin formation and maintenance, with wide-ranging implications for normal cells and disease.

Animals↗
PubMedDate not supplied

Reciprocal translocation between Y chromosome long arm euchromatin and the short arm of chromosome 1.

A case with an apparently balanced reciprocal translocation between the long arm of the Y chromosome and the short arm of chromosome 1 t(Y;1)(q11.2;p34.3) is described. The translocation was found in a phenotypically normal male ascertained by infertility and presenting for intra-cytoplasmatic sperm injection treatment. Histological examination of testicular biopsies revealed spermatogenic failure. Chromosome painting with probes for chromosome 1 and for the euchromatic part of the Y chromsome confirmed the translocation of euchromatic Y chromosomal material onto the short arm of chromosome 1 and of a substantial part of the short arm of chromosome 1 onto the Y chromosome. Among the Y/autosome translocations, the rearrangements involving long arm euchromatin of the Y chromosome are relatively rare and mostly associated with infertility. Microdeletion screening at the azoospermia locus revealed no deletions, suggesting another mechanism causing infertility in this translocation carrier.

Adult↗
PubMed2001

Modelling chromosomal aberration induction by ionising radiation: the influence of interphase chromosome architecture.

Several advances have been achieved in the knowledge of nuclear architecture and functions during the last decade, thus allowing the identification of interphase chromosome territories and sub-chromosomal domains (e.g. arm and band domains). This is an important step in the study of radiation-induced chromosome aberrations; indeed, the coupling between track-structure simulations and reliable descriptions of the geometrical properties of the target is one of the main tasks in modelling aberration induction by radiation, since it allows one to clarify the role of the initial positioning of two DNA lesions in determining their interaction probability. In the present paper, the main recent findings on nuclear and chromosomal architecture are summarised. A few examples of models based on different descriptions of interphase chromosome organisation (random-walk models, domain models and static models) are presented, focussing on how the approach adopted in modelling the target nuclei and chromosomes can influence the simulation of chromosomal aberration yields. Each model is discussed by taking into account available experimental data on chromosome aberration induction and/or interphase chromatin organisation. Preliminary results from a mechanistic model based on a coupling between radiation track-structure features and explicitly-modelled, non-overlapping chromosome territories are presented.

Animals↗
PubMed1999

Differentiation of Z and W chromosomes revealed by replication banding and FISH mapping of sex-chromosome-linked DNA markers in the cassowary (Aves, Ratitae).

We identified sex chromosomes of the double-wattled cassowary (Casuarius casuarius) by a replication banding method. The acrocentric Z chromosome, the fifth largest pair in males and slightly smaller W chromosome show no sign of heterochromatinization and share a nearly identical banding pattern in the distal half of the long arm. These chromosomes were further characterized by FISH with three probes linked either to Z or W chromosome in most avian species examined thus far. Contrary to the situation in the chicken, we obtained positive signals with Z-specific ZOV3 and W-specific EEO.6 in the distal region of both Z and W chromosomes. However, IREBP signals localized to the proximal half of the Z chromosome were not detected on the W chromosome. Thus, structural rearrangements such as deletions and inversions might have been the initial step of W chromosome differentiation from an ancestral homomorphic pair in this species.

Animals↗