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PubMed2005

European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations (ECARUCA); an online database for rare chromosome abnormalities.

During recent years a considerable improvement in diagnostic techniques has enabled cytogeneticists to find more and smaller chromosomal aberrations. However, accurate clinical knowledge about rare chromosome disorders is frequently lacking, mostly due to a significant decline in publishable cases. On the other hand, there is an increasing demand from parents and physicians for reliable information. In order to improve the quality and the quantity of data available, we designed a new database named the European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations (ECARUCA) at http://www.ecaruca.net. This Internet-database contains cytogenetic and clinical data of patients with rare chromosome abnormalities, including microscopically visible aberrations, as well as microdeletions and -duplications. Cases with certain breakpoints collected in the Zurich Cytogenetic Database were transferred to ECARUCA. The advantages of ECARUCA compared to existing sources are that ECARUCA is interactive, dynamic and has long-term possibilities to store cytogenetic, molecular and clinical data. Professionals can login to submit new cases and perform searches in the database through the Internet. Currently the database contains 1500 unique chromosomal aberrations from almost 4000 patients. A frequent submission of new data ensures the up-to-date quality of the collection. Individual parent accounts allow parents to inform the ECARUCA team about the follow-up of their child. The ECARUCA database provides health care workers with accurate information on clinical aspects of rare chromosome disorders. Additionally, detailed correlations between chromosome aberrations and their phenotypes are of invaluable help in localising genes for mental retardation and congenital anomalies.

Chromosome Aberrations↗
PubMed1998

Condensation pattern (CP) analysis of plant chromosomes by an improved chromosome image analysing system, CHIAS III.

The third-generation chromosome image analysing system (CHIAS III) was developed by using an ordinary personal computer with public domain imaging software, the NIH Image. An uneven condensation pattern (CP) appearing on small sugarcane chromosomes at the mitotic prometaphase stage was analysed and a quantitative chromosome map or idiogram was developed by using CHIAS III. The analysis consists of three major steps as follows: (1) manipulation of original chromosome images and measurement of CP or numerical data of the CP; (2) calculation of an averaged CP for homologous chromosomes; and (3) development of an idiogram based on the averaged CP. The CP has been analysed quantitatively by using the first- and the second-generation chromosome image analysing systems with hard- and software specific to the systems. The data obtained using CHIAS III are consistent with those obtained with the chromosome image analysing systems previously developed.

Chromosomes↗
PubMed2000

Cytogenetic characterization of a supernumerary chromosome segment and of B-chromosomes in Astyanax scabripinnis (Teleostei, Characidae).

The chromosome complement of a local population of Astyanax scabripinnis in Brazil was investigated with emphasis on the study of the heterochromatin attached to the A-chromosomes and present in the macro B-chromosome. Analysis after C-banding, silver and CMA3 staining, incorporation of 5-bromo-2'-deoxyuridine and chromosome digestion with nine restriction endonucleases revealed that the heterochromatin in the B-chromosomes was different from that found in the A-chromosomes. A polymorphism due to the presence of a supernumerary heterochromatic chromosome segment was observed in the population investigated. Some aspects related to the origin of the heterochromatin polymorphism in Astyanax scabripinnis are discussed.

Animals↗
PubMed2002

Differential effects of cultivated and wild barley 5H chromosomes on heading characters in wheat-barley chromosome addition lines.

Wheat (Triticum aestivum L.)-barley (Hordeum vulgare L.) chromosome addition lines are possible vehicles for transferring barley genes into wheat. The barley 5H chromosome has genetic effects on the heading characters in wheat-barley addition lines: accelerating narrow-sense earliness, decreasing vernalization requirement and/or increasing photoperiodic sensitivity. To elucidate the effects of different 5H chromosomes under an identical wheat genetic background, two wheat-barley addition lines, i.e. cultivated barley 'New Golden' 5H chromosome added to 'Shinchunaga' wheat (Shi-NG5H) and wild barley H. vulgare ssp. spontaneum 5H chromosome added to 'Shinchunaga' wheat (Shi-Spn5H), were examined for their heading characters. The addition line Shi-NG5H showed a significantly lower vernalization requirement in comparison with 'Shinchunaga' wheat, whereas Shi-Spn5H did not. Furthermore, both NG5H and Spn5H chromosomes shortened narrow-sense earliness and increased photoperiodic sensitivity in wheat, but the effects of Spn5H were weaker than those of NG5H. The fact that NG5H and Spn5H showed differential effects on heading characters in wheat demonstrated that the heading characters were altered by the function of the barley genes located on 5H chromosomes, not merely by the aneuploid effect alone.

Chromosomes, Plant↗
PubMed1984

Methylation of the hypoxanthine phosphoribosyltransferase locus on the human X chromosome: implications for X-chromosome inactivation.

To explore the role of DNA methylation in maintaining dosage compensation of X chromosome-linked genes and in regulating the transcriptional activity of "housekeeping" genes, we characterized DNA methylation of active, inactive, and derepressed alleles at the locus for hypoxanthine phosphoribosyltransferase (HPRT) on the human X chromosome. The methylation of Hpa II and Hha I sites in HPRT alleles on the active X chromosome was the same in all tissues. The consensus pattern includes hypomethylation of 5' clustered sites and extensive methylation of the 3' sequence. The striking feature of methylation of inactive X-chromosome alleles is nonuniformity and less extensive hypomethylation of the 5' cluster. Analysis of HPRT alleles reactivated in response to 5-azacytidine showed at least partial restoration of the consensus pattern. These observations indicate that methylation of housekeeping genes on the X chromosome is the same as that of autosomal ones and that the overall pattern and methylation of multiple sites within a cluster may cooperate to facilitate transcription. Furthermore, the fidelity of methylation of the active allele and the extensive drift in methylation of the inactive allele suggest that mechanisms involved in X-chromosome dosage compensation may be directed at the active rather than inactive X chromosome.

Alleles↗
PubMed1996

Analysis of radiation-induced chromosome aberrations in Chinese hamster cells by FISH using chromosome-specific DNA libraries.

The frequencies of chromosome aberrations induced by different doses of X-rays were determined in both splenocytes and primary lung fibroblasts of Chinese hamster by bi-colour FISH using a combination of four chromosome-specific DNA libraries. The results indicate that the X-rays induced more translocations than dicentrics in Chinese hamster cells, in which the karyotype is comprised of both metacentric and acrocentric chromosomes. These results are similar to those reported in human lymphocytes, in which the karyotype contains many metacentric chromosomes. On the contrary, in mouse, which is characterized by acrocentric chromosomes only, the frequencies of translocations and dicentrics are induced in nearly equal proportions by X-rays. The ratio of translocations to dicentrics obtained in Chinese hamster cells was approximately 1.4-1.5, which supports the importance of the karyotypic features of a species in the relative induction of translocations to dicentrics. An analysis was also made on the yield of translocations and dicentrics involving individual chromosomes and the results indicate a non-random involvement of these chromosomes in the formation of aberrations.

Animals↗
PubMed1997

Topoisomerase II inhibitors fail to induce chromosome-type aberrations in etoposide-resistant cells: evidence for essential contribution of the cleavable complex formation to the induction of chromosome-type aberrations.

The induction of chromosome-type aberrations is mediated by stabilization of the DNA-topoisomerase II (topo-II) complex, the cleavable complex (CC), induced by topo-II inhibitors. In the present study, in order to confirm the critical contribution of topo-II in producing chromosome-type aberrations, the inducibility of chromosome-type aberrations by topo-II inhibitors was compared between human epidermoid cancer KB cells and their mutant cells (KB/ VP-2 cells) which were resistant to etoposide (VP-16) and which have reduced levels of topo-II and its gene expression. KB/VP-2 cells were resistant to the cytotoxicity of topo-II inhibitors and most resistant to etoposide. In KB cells treated with etoposide which had accumulated CC, chromosome-type aberrations but not chromatid-type aberrations were efficiently induced, as has already been reported in Chinese hamster fibroblasts. In contrast, in KB/VP-2 cells with no accumulation of CC, etoposide induced mainly chromatid-type aberrations, with a few chromosome-type aberrations. Unlike etoposide, however, adriamycin, which was known to accumulate CC in Chinese hamster fibroblastic cells, neither induced chromosome-type aberrations nor accumulated CC in either KB or KB/VP-2 cells. No difference in cell incorporation of [3H]etoposide between the two cell lines was observed. These findings indicate that CC formation contributes to the induction of chromosome-type aberrations, although the reason why adriamycin could not accumulate CC in KB cells is not clear. This may suggest a mechanism for resistance to topo-II inhibitors in cancer chemotherapy.

Antineoplastic Agents, Phytogenic↗
PubMed1992

Construction of a chromosome-enriched HpaII library from flow-sorted wheat chromosomes.

We report here the first successful generation of a chromosome-enriched library from flow sorted plant chromosomes. Chromosomes with a characteristic DNA content (a peak) were sorted from a synchronized cell culture (TaKB1, derived from Triticum aestivum). A HpaII library was constructed from the sorted chromosomes and half of the cloned DNA sequences analysed are unique or low copy. Approximately half of these sequences when used as probes detect sequences on wheat chromosome 4A. The generation and analysis of the chromosome library is described in detail and the prospects of using flow-sorted plant chromosomes discussed.

Cells, Cultured↗
PubMed1998

Repetitive sequences (RPSs) in the chromosomes of Candida albicans are sandwiched between two novel stretches, HOK and RB2, common to each chromosome.

A novel sequence designated HOK, which is next to the RPS, a repetitive sequence specific to Candida albicans, was cloned and sequenced. HOK hybridized with all of the chromosomes on which the RPSs were located, but did not hybridize with chromosome 3, which does not harbour any RPSs. Sequence determination revealed that a portion of HOK has significant homology with the B and C1 fragments of Ca3, which is used as a molecular epidemiological probe. A homology search of the deduced amino acids of HOK against the protein database showed partial homology with an isocitrate dehydrogenase of Saccharomyces cerevisiae, although an ORF large enough to encode the enzyme was not detected. To verify the existence of other sequences homologous with HOK, a portion of the HOK sequence was amplified using PCR. Sequence determination of the 41 clones from the PCR products resulted in at least six HOK-homologous clones. Another RPS-containing clone, RB2, was isolated from the Pstl-digested chromosome R or 1. It was determined that RB2a, one of the subclones from RB2, hybridized with all of the chromosomes, including chromosome 3, with which neither HOK nor RPS hybridized. The hybridization profile also showed that RPS is located between HOK and RB2a on chromosomes other than chromosome 3.

Candida albicans↗
PubMed2003

In vivo requirements for rDNA chromosome condensation reveal two cell-cycle-regulated pathways for mitotic chromosome folding.

Chromosome condensation plays an essential role in the maintenance of genetic integrity. Using genetic, cell biological, and biochemical approaches, we distinguish two cell-cycle-regulated pathways for chromosome condensation in budding yeast. From G(2) to metaphase, we show that the condensation of the approximately 1-Mb rDNA array is a multistep process, and describe condensin-dependent clustering, alignment, and resolution steps in chromosome folding. We functionally define a further postmetaphase chromosome assembly maturation step that is required for the maintenance of chromosome structural integrity during segregation. This late step in condensation requires the conserved mitotic kinase Ipl1/aurora in addition to condensin, but is independent of cohesin. Consistent with this, the late condensation pathway is initiated during the metaphase-to-anaphase transition, supports de novo condensation in cohesin mutants, and correlates with the Ipl1/aurora-dependent phosphorylation of condensin. These data provide insight into the molecular mechanisms of higher-order chromosome folding and suggest that two distinct condensation pathways, one involving cohesins and the other Ipl1/aurora, are required to modulate chromosome structure during mitosis.

Adenosine Triphosphatases↗
PubMed2004

Evolutionary strata on the mouse X chromosome correspond to strata on the human X chromosome.

Lahn and Page previously observed that genes on the human X chromosome were physically arranged along the chromosome in "strata," roughly ordered by degree of divergence from related genes on the Y chromosome. They hypothesized that this ordering results from a historical series of suppressions of recombination along the mammalian Y chromosome, thereby allowing formerly recombining X and Y chromosomal genes to diverge independently. Here predictions of this hypothesis are confirmed in a nonprimate mammalian order, Rodentia, through an analysis of eight gene pairs from the X and Y chromosomes of the house mouse, Mus musculus. The mouse X chromosome has been rearranged relative to the human X, so strata were not found in the same physical order on the mouse X. However, based on synonymous evolutionary distances, X-linked genes in M. musculus fall into the same strata as orthologous genes in humans, as predicted. The boundary between strata 2 and 3 is statistically significant, but the boundary between strata 1 and 2 is not significant in mice. An analysis of smaller fragments of Smcy, Smcx, Zfy, and Zfx from seven species of Mus confirmed that the strata in Mus musculus were representative of the genus Mus.

Animals↗
PubMed2004

Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements.

We have investigated the fluidity of the Salmonella chromosome architecture using the phage lambda site-specific recombination system as a probe. We determined how chromosome position affects the extent of integrase-mediated recombination between pairs of inversely oriented att sites at various loci. We also investigated the accessibility of each chromosomal att site to an extrachromosomal partner carried on a low-copy plasmid. Recombination events were assayed by semi-quantitative polymerase chain reaction of the attP product. The extent of recombination between the chromosome and the plasmid was generally higher than intrachromosomal recombination except for two loci, araA::attL and galT::attL, which gave no detectable recombination with any other locus. Based on 20 intervals, we found that chromosomal locations are not equally accessible to each other. Although multiple factors probably affect accessibility, the most important is the specific combination of the end-points used. Neither the size of the intervals nor the accessibility of individual end-points to extrachromosomal sequences is as important. These results suggest that the chromosome is not completely fluid but rather organized in some way, with barriers that limit the movement of DNA within the cell. The nature of the barriers involved in chromosomal organization remains to be determined.

Attachment Sites, Microbiological↗
PubMed1997

Supernumerary marker chromosomes (SMCs) in Turner syndrome are mostly derived from the Y chromosome.

DNA and FISH (fluorescence in situ hybridization) analysis were carried out in 12 patients with stigmata of Turner syndrome to determine whether the Supernumerary Marker Chromosome (SMC) found cytogenetically in each of these patients was derived from the Y chromosome. The presence of a Y chromosome in these patients may predispose them to develop gonadoblastoma. PCR-Southern blot analysis, followed by FISH, was used to detect the presence of Y chromosome material. The Sex determining Region Y (SRY), Testis Specific Protein Y-encoded (TSPY) and Y-chromosome RNA Recognition Motif (YRRM) genes, which map at Yp11.31, Yp11.1-11.2 and Yp11.2/Yq11.21-11.23, respectively, were selected as markers, because they span the whole Y chromosome, and more importantly, they are considered to be involved in the development of gonadoblastoma. It was shown that in 12 patients, all of whom had an SMC, the SMC of 11 was derived from the Y chromosome. Furthermore, the presence of the SRY, TSPY and YRRM gene sequences was determined and FISH analysis confirmed the Y origin of the SMCs. The methodology described in this report is a rapid, reliable and sensitive approach which may be easily applied to determine the Y origin of an SMC carried in Turner syndrome. The identification of an SMC is important for the clinical management and prognostic counseling of these patients with Turner syndrome.

Cell Cycle Proteins↗
PubMed1995

Precise spatial positioning of chromosomes during prometaphase: evidence for chromosomal order.

The relative locations of several chromosomes within wheel-shaped prometaphase chromosome rosettes of human fibroblasts and HeLa cells were determined with fluorescence hybridization. Homologs were consistently positioned on opposite sides of the rosette, which suggests that chromosomes are separated into two haploid sets, each derived from one parent. The relative locations of chromosomes on the rosette were mapped by dual hybridizations. The data suggest that the chromosome orders within the two haploid sets are antiparallel. This chromosome arrangement in human cells appears to be both independent of cell type- and species-specific and may influence chromosome topology throughout the cell cycle.

Cells, Cultured↗
PubMed2004

Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC.

Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element composed of the mec gene complex, which encodes methicillin resistance, and the ccr gene complex, which encodes the recombinases responsible for its mobility. The mec gene complex has been classified into four classes, and the ccr gene complex has been classified into three allotypes. Different combinations of mec gene complex classes and ccr gene complex types have so far defined four types of SCCmec elements. Now we introduce the fifth allotype of SCCmec, which was found on the chromosome of a community-acquired methicillin-resistant Staphylococcus aureus strain (strain WIS [WBG8318]) isolated in Australia. The element shared the same chromosomal integration site with the four extant types of SCCmec and the characteristic nucleotide sequences at the chromosome-SCCmec junction regions. The novel SCCmec carried mecA bracketed by IS431 (IS431-mecA-DeltamecR1-IS431), which is designated the class C2 mec gene complex; and instead of ccrA and ccrB genes, it carried a single copy of a gene homologue that encoded cassette chromosome recombinase. Since the open reading frame (ORF) was found to encode an enzyme which catalyzes the precise excision as well as site- and orientation-specific integration of the element, we designated the ORF cassette chromosome recombinase C (ccrC), and we designated the element type V SCCmec. Type V SCCmec is a small SCCmec element (28 kb) and does not carry any antibiotic resistance genes besides mecA. Unlike the extant SCCmec types, it carries a set of foreign genes encoding a restriction-modification system that might play a role in the stabilization of the element on the chromosome.

Amino Acid Sequence↗
PubMed2004

Two chimeric chromosomes of Streptomyces coelicolor A3(2) generated by single crossover of the wild-type chromosome and linear plasmid scp1.

Streptomyces coelicolor A3(2) strain 2106 carries a 1.85-Mb linear plasmid, SCP1'-cysD, in addition to a 7.2-Mb linear chromosome. Macrorestriction analysis indicated that both linear DNAs are hybrids of the wild-type chromosome and the linear plasmid SCP1 on each side. Nucleotide sequencing of the fusion junctions revealed no homology between the recombination regions. SCP1'-cysD contains an SCP1 telomere and a chromosomal telomere at each end and therefore does not have terminal inverted repeats. In addition, SCP1'-cysD could not be eliminated from strain 2106 by various mutagenic treatments. Thus, we concluded that both the 7.2-Mb chromosome and SCP1'-cysD are chimeric chromosomes generated by a single crossover of the wild-type chromosome and SCP1. This may be regarded as a model of chromosomal duplication in genome evolution.

Amino Acid Sequence↗
PubMed2005

The mitotic chromosome binding activity of the papillomavirus E2 protein correlates with interaction with the cellular chromosomal protein, Brd4.

The papillomavirus transcriptional activator, E2, is involved in key functions of the viral life cycle. These include transcriptional regulation, viral DNA replication, and viral genome segregation. The transactivation domain of E2 is required for each of these functions. To identify the regions of the domain that mediate binding to mitotic chromosomes, a panel of mutations has been generated and their effect on various E2 functions has been analyzed. A structural model of the bovine papillomavirus type 1 (BPV1) E2 transactivation domain was generated based on its homology with the solved structure of the human papillomavirus type 16 (HPV16) domain. This model was used to identify distinct surfaces of the domain to be targeted by point mutation to further delineate the functional region of the transactivation domain responsible for mitotic chromosome association. The mutated E2 proteins were assessed for mitotic chromosome binding and, in addition, transcriptional activation and transcriptional repression activities. Mutation of amino acids R37 and I73, which are located on a surface of the domain that in HPV16 E2 is reported to mediate self-interaction, completely eliminated mitotic chromosome binding. Mitotic chromosome binding activity was found to correlate well with the ability to interact with the cellular chromosomal associated factor Brd4, which has recently been proposed to mediate the association between BPV1 E2 and mitotic chromosomes.

Animals↗
PubMed2005

Molecular cytogenetic identification of nullisomy 5B induced homoeologous recombination between wheat chromosome 5D and barley chromosome 5H.

Chromosome 5H of Hordeum vulgare 'New Golden' (NG) carries a gene(s) that accelerates heading in a wheat background. To introduce the early heading gene(s) of NG barley into the wheat genome, we attempted to induce homoeologous recombination between wheat and NG 5H chromosomes by 5B nullisomy. A nullisomic 5B, trisomic 5A, monosomic 5H plant (2n = 42) was produced from systematic crosses between aneuploid stocks of wheat group 5 chromosomes. A total of 656 F2 plants produced by self-fertilization were screened for recombinants by a PCR assay with 3 5H-specific amplicon markers. Twelve plants (1.8%) were selected as putative wheat-barley 5H recombinants. Five of them were inviable or sterile and the remaining 7 were fertile and subjected to the progeny test. Cytological analyses using fluorescence in situ hybridization and C-banding revealed that 6 of the 7 progeny lines are true homoeologous recombinants between the long arms of chromosomes 5D and 5H, but that the other one was not a recombinant having an aberrant barley telosome. The 6 cytologically confirmed recombinant lines included only 2 types (3 lines each), which were reciprocal products derived from exchanges at the same distal interval defined by two flanking markers. One type had a small 5HL segment translocated to the 5DL terminal, and the other type had a small terminal 5DL segment translocated to the 5HL terminal. In the latter type, the physical length of translocated barley segments slightly differed among lines. Homoeologous recombinants obtained in this study should be useful for further chromosome manipulation to introgress a small interstitial 5HL chromosome segment with the early heading gene(s) to wheat. Preferential occurrence of restricted types of recombinants is discussed in relation to homoeologous relationships between wheat and barley chromosomes.

Aneuploidy↗