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Results for “Chromosome segmentation”

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PubMed2004

Refined genotype-phenotype correlations in cases of chromosome 6p deletion syndromes.

Clinical reports of cases with deletions in chromosome 6p are relatively rare. We present a detailed study by fluorescent in situ hybridisation (FISH) of six new cases with distinct but overlapping 6p deletions involving the 6p24-pter chromosomal segment. Chromosomal breakpoints in individual cases were investigated using a large panel of probes previously mapped and characterised in our laboratory to cover the distal region of 6p. These cases have allowed refinement of genotype-phenotype correlations and strongly suggest a gene involved in regulating the development of hearing is localised within 6p25. There is also evidence for one or more loci involved in heart, skeletal and craniofacial development in the 6p24-p25 region. Furthermore, the Dandy-Walker malformation is associated with deletion of 6p24-pter.

Abnormalities, Multiple↗

PubMed2001

[Key technologies in image analysis of comparative genomic hybridization].

Comparative genomic hybridization has become a new technique in molecular-cytogenetics, and it has found significant applications in tumor pathology. Image analysis is an important part of comparative genomic hybridization. It analyzes the fluorescent images by many steps and finally determines whether there is any abnormality in the copy number of the test tumor tissue. This paper expatiates on the key steps in the image analysis of comparative genomic hybridization, including background correction, chromosome segmentation, chromosome axis determination, karyotyping and determining ratio profile. The future trend is also discussed.

Cytogenetics↗

PubMed2005

Maximum-likelihood techniques for joint segmentation-classification of multispectral chromosome images.

Traditional chromosome imaging has been limited to grayscale images, but recently a 5-fluorophore combinatorial labeling technique (M-FISH) was developed wherein each class of chromosomes binds with a different combination of fluorophores. This results in a multispectral image, where each class of chromosomes has distinct spectral components. In this paper, we develop new methods for automatic chromosome identification by exploiting the multispectral information in M-FISH chromosome images and by jointly performing chromosome segmentation and classification. We (1) develop a maximum-likelihood hypothesis test that uses multispectral information, together with conventional criteria, to select the best segmentation possibility; (2) use this likelihood function to combine chromosome segmentation and classification into a robust chromosome identification system; and (3) show that the proposed likelihood function can also be used as a reliable indicator of errors in segmentation, errors in classification, and chromosome anomalies, which can be indicators of radiation damage, cancer, and a wide variety of inherited diseases. We show that the proposed multispectral joint segmentation-classification method outperforms past grayscale segmentation methods when decomposing touching chromosomes. We also show that it outperforms past M-FISH classification techniques that do not use segmentation information.

Algorithms↗

PubMed2006

Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements.

Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make orthologous gene pairs difficult to identify and because colinearity is expected to be low with greater time since divergence from the last common ancestor. Nevertheless, synteny between divergent taxa in several lineages has been detected over short chromosomal segments. We have examined the level of synteny between the model species Arabidopsis thaliana and species in the Compositae, one of the largest and most diverse plant families. While macrosyntenic patterns covering large segments of the chromosomes are not evident, significant levels of local synteny are detected at a fine scale covering segments of 1-Mb regions of A. thaliana and regions of <5 cM in lettuce and sunflower. These syntenic patches are often not colinear, however, and form a network of regions that have likely evolved by duplications followed by differential gene loss.

Arabidopsis↗

PubMed1994

Segmental tetrasomy of chromosome 12 in the mouse.

An inbred strain of mice has been identified that is homozygous for a chromosomal segment attached to the centromeric region of Chromosome (Chr) 5. The altered chromosome arose spontaneously, and it does not appear to interfere with fertility or to have a phenotypic effect. Karyotypic analysis based on G-banding and quinacrine/Hoechst-banding studies revealed a morphological similarity between the additional segment of Chr 5 and the centromeric region of Chr 12. The mutant strain possessed silver-stainable nucleolar organizer regions, not only in the centromeric regions of Chrs 12, 15, and 18 but also on the additional segment of Chr 5. We investigated the relationship between the additional segment and the restriction fragment length polymorphisms (RFLPs) for the variable region of ribosomal DNA and found a correlation between a HincII RFLP and either the abnormal Chr 5 or Chr 12. These results indicate that the origin of the additional segment was Chr 12 and that the segmental tetrasomy of the present strain is therefore due to a nondetrimental translocation between pericentromeric regions.

Aneuploidy↗

PubMed1999

Significant differences in the frequency of transcriptional units, types and numbers of repetitive elements, GC content, and the number of CpG islands between a 1010-kb G-band genomic segment on chromosome 9q31.3 and a 1200-kb R-band genomic segment on chromosome 3p21.3.

We determined the nucleotide sequence of the entire 1,010,525-bp insert contained in CEPH YAC clone 867e8. This human genomic segment was derived from chromosome 9q31.3 and corresponds to a G-band region. We compared this segment, in terms of structure, with a previously characterized 1,201,033-bp sequence in CEPH YAC936c1 that had come from a portion of human chromosome 3p21.3 corresponding to an R-band region. The two segments were significantly different with respect to the frequency of transcriptional units, the types and numbers of repetitive elements present, their GC content, and the number of CpG islands. Alu elements, GC content, and CpG islands all showed positive correlations with the abundance of exons, but the distribution of LINE1s did not. These observations might reflect an influence of the first three of these features on the functions or expression of genes in the respective regions. In addition to a novel gene (F36) lying at the centromeric end of the 9q segment, we found a cluster of placenta-specific genes within a small section (about 400 kb) on the telomeric side of YAC867e8. This cluster consisted of four apparently unrelated ESTs and two genes, pregnancy-associated plasma protein-A (PAPP-A) and a novel gene (tentatively named EST-YD1). Our characterization of the two chromosomal regions provided evidence that genes are not evenly distributed throughout the human genome, and that gene richness is correlated with the GC content and with the frequency of either Alu elements or CpG islands.

Alu Elements↗

PubMed1976

Segmentation of human chromosomes induced by 5-ACR (5-azacytidine).

The 5-ACR (5-azacytidine) introduced in human lymphocyte cultures induces a lack or a delay of condensation of some chromosome segments corresponding to the G-bands. The resulting R-banding is very similar to that obtained with a 7-h treatment by BrdU, although the segmentation may be much stronger (pulverization) with high doses. However, the 5-ACR does not induce chromatid asymmetry, as BrdU does. This constitutes a new argument for considering that the segmentation and the asymmetry of chromatids depend, at least partly, on two different mechanisms, where proteins are probably involved. Another effect of 5-ACR is to increase chromosome associations by satellites, secondary constrictions, and telomeric regions.

Azacitidine↗

PubMed2003

Chromosomal territory segmentation in apoptotic cells.

The nuclear architecture of selected chromosomes in apoptotic nuclei of human leukemic cells K-562 and HL-60 was investigated. Etoposide and prolonged confluence were used for the induction of apoptosis. DAPI as well as TUNEL labeling of apoptotic nuclear bodies was combined with visualization of chromosomal territories by the FISH technique. Simultaneous vital staining by annexin V, propidium iodide, and Hoechst 33342 was applied to distinguish apoptotic, necrotic, and intact cell fraction of tested populations. Our FISH analyses revealed that the three-dimensional (3D) structure of apoptotic nuclei as well as the 3D structure of apoptotic bodies is preserved in formaldehyde-fixed cells. High-molecular-weight DNA fragmentation was determined in apoptotic K-562 cells in contrast to oligonucleosomal cleavage observed in apoptotic HL-60 cells. In K-562 populations, chromosomal territories were located separately either in one apoptotic body or underwent disassembly into chromosomal segments dispersed into single and/or several apoptotic bodies. The apoptotic disorganization of chromosomal territories was irregular, leading mainly to chromosomal segments of different sizes and, consequently, chromosomal disassembly was not observed at specific sites. In comparison with the control, an increased number of centromeric FISH signals were observed in prolonged confluence-treated K-562 cells induced to apoptosis. This finding can be explained either as a consequence of apoptosis or by polyploidization. Sequential staining of the same apoptotic nuclei by the FISH and TUNEL techniques revealed that chromosomal territory segmentation precedes the formation of nuclear apoptotic bodies.

Apoptosis↗

PubMed1995

Marker enrichment and high-resolution map of the segment of potato chromosome VII harbouring the nematode resistance gene Gro1.

The dominant allele Gro1 confers on potato resistance to the root cyst nematode Globodera rostochiensis. The Gro1 locus has been mapped to chromosome VII on the genetic map of potato, using RFLP markers. This makes possible the cloning of Gro1 based on its map position. As part of this strategy we have constructed a high-resolution genetic map of the chromosome segment surrounding Gro1, based on RFLP, RAPD and AFLP markers. RAPD and AFLP markers closely linked to Gro1 were selected by bulked segregant analysis and mapped relative to the Gro1 locus in a segregating population of 1105 plants. Three RFLP and one RAPD marker were found to be inseparable from the Gro1 locus. Two AFLP markers were identified that flanked Gro1 at genetic distances of 0.6 cM and 0.8 cM, respectively. A genetic distance of 1 cM in the Gro1 region corresponds to a physical distance of ca. 100 kb as estimated by long-range restriction analysis. Marker-assisted selection for nematode resistance was accomplished in the course of constructing the high-resolution map. Plants carrying the resistance allele Gro1 could be distinguished from susceptible plants by marker assays based on the polymerase chain reaction (PCR).

Animals↗

PubMed1976

Frequency of chromosomal fluorescence polymorphism in normal persons and in clinical patients with diagnosed chromosome aberrations.

By means of a computer program the frequencies of the strongly fluorescent polymorphous chromosomal segments on chromosomes Nos. 3, 4, 13, 14, 15, 21, and 22 among 89 random normal persons and 247 persons suspected of having various chromosome aberrations were determined. It was discovered that: 1. In none of the 13 diagnosis categories are divergencies in frequency of autosomal fluorescence polymorphism, as compared to the normal group, statistically determinable. 2. A worthwhile comparison of the various frequencies of fluorescence polymorphism as recorded by the various investigators in not possible at present, since the applied methods of assessment differ too widely. 3. Standardization of the criteria of assessment and of the nomenclature for the polymorphous chromosomal segment would seem to be a matter of urgent necessity.

Chromosome Aberrations↗

PubMed2001

Congenic BB.SHR rat provides evidence for effects of a chromosome 4 segment (D4Mit6-Npy approximately 1 cm) on total serum and lipoprotein lipid concentration and composition after feeding a high-fat, high-cholesterol diet.

Congenic BB.SHR (previously referred to as BB.LL) rats were generated by transferring the segment of chromosome 4 flanked by the D4Mit6 and Spr loci from the spontaneously hypertensive rat (SHR/Mol) onto the genetic background of the diabetes-prone BB/OK rat. In this study, the influence of the above-mentioned region of chromosome 4 on triglyceride, cholesterol, and phospholipid phenotypes after a high-fat, high-cholesterol diet was examined by comparison of BB.SHR congenic rats with BB/OK rats. BB/OK and BB.SHR had comparable concentrations of basal and postdietary serum insulin, as well as of basal total serum triglycerides and had an identical body weight and food intake at the beginning of the test period. However, after 4 weeks on the test diet, BB.SHR rats were significantly heavier than BB/OK rats and had significantly higher food intake and lower total serum triglyceride concentrations. The basal serum leptin level was significantly lower, but postdietary serum leptin concentration did not show a significant difference between the 2 strains. Furthermore, significantly higher basal total serum cholesterol and phospholipid levels were observed in BB.SHR rats, but this difference disappeared after feeding the high-fat, high-cholesterol diet. Postdietary high-density lipoprotein (HDL)(2) cholesterol and phospholipid levels were significantly elevated in BB.SHR rats when compared with BB/OK rats. The 2 strains also differed slightly, but significantly, with respect to the other HDL phospholipid concentrations. In addition to previously described differences between BB/OK and BB.SHR rats, the results of this study clearly show the impact of genes, lying within the transferred segment, on serum lipid phenotypes after high-fat, high-cholesterol diet.

Alleles↗

PubMed1983

Induction of leukemia by both fractionated x-irradiation and radiation leukemia virus involves loci in the chromosome 2 segment H-30-A.

A common link between the induction of leukemia by (i) fractionated doses of x-irradiation and (ii) radiation leukemia virus in mice may be established by the observation that the segment of chromosome 2 between the loci for the minor histocompatibility antigen H-30 and color coat agouti (H-30-A) includes distinct loci involved in susceptibility to leukemogenesis induced by factors i and ii.

Animals↗

PubMed1998

Vertebrate genome evolution and the zebrafish gene map.

In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence.

Animals↗

PubMed2004

Contribution of chromosomal imbalance to sperm selection and pre-implantation loss in translocation-heterozygous Chinese hamsters.

Chinese hamster stocks with various structurally abnormal chromosomes have been produced by X irradiation. Among these stocks, 18 with various reciprocal translocations were used to investigate the participation of unbalanced gametes in fertilization and the development of unbalanced embryos. Among males as well as females heterozygous for the same translocation, there is no difference in the frequency of each disjunctional class. The participation of chromosomally unbalanced gametes in fertilization was investigated by chromosomal analysis of meiotic cells in heterozygotes for the 18 reciprocal translocations and pronuclei of fertilized ova obtained from crossing these heterozygotes. Compared with the expected frequencies from MII scoring, the frequencies of male pronuclei having a common deficiency of chromosome 1 (1q17-->1q42) or chromosome 3 (3p23-->3q31) decreased significantly in one-cell embryos. However, the frequencies of male pronuclei with other abnormalities were all consistent with those expected from MII scoring. In contrast, the frequencies of female pronuclei with any karyotype including the same abnormalities as those decreased in male pronuclei from the translocation heterozygotes were all consistent with those estimated from MII scoring. These results revealed clearly that most gametes with nullisomies as well as disomies for any chromosomal segments may participate in fertilization, whereas only male gametes nullisomic for certain segments of chromosomes 1 and 3 failed to participate in fertilization. The zygotic selection of chromosomal imbalance was also investigated by direct chromosomal and morphological analyses of preimplantation embryos from crosses between karyotypically normal females and male heterozygotes from the 18 stocks with various reciprocal translocations. These analyses revealed that some embryos were arrested in development at the two-cell stage. The karyotype of these two-cell embryos had a common deficiency in a segment of chromosome 1 or chromosome 2. Embryos with partial monosomy including chromosomes 1, 3, 4 and 5 showed arrested development at four- to eight-cell stages. Among day 4 embryos, some chromosomally unbalanced embryos, mainly with a deficiency of segments of chromosomes 1p, 1q, 2q, 5q, 7q and 8, had fewer blastomeres than karyotypically normal and balanced embryos. The homology between Chinese hamster and mouse chromosomes relating to abnormal embryogenesis at early stages has been partially confirmed from reported maps of chromosomes. The Chinese hamster is useful for further cytogenetic studies during the stages of meiosis and early embryogenesis.

Aneuploidy↗

PubMed2003

Evolutionary dynamics of duplicated microsatellites shared by sex chromosomes.

Segmental duplications on sex chromosomes constitute an important proportion of recent duplications (approximately 30%). Among those, the evolution of duplicated noncoding DNA is still poorly investigated. We focus our work on repeated DNA sequences extensively used in population genetics and evolution: microsatellites. Six duplicated (CA), microsatellite loci, located on the homologous region of human sex chromosomes, were studied at the intraspecific level in Homo sapiens and by an orthologous comparison in eight primate species. At the intraspecific level, we evaluated the congruence in paralogous divergence between the flanking sequences of the six microsatellites and the approximately 2.2-kb surrounding sequences and observed that both phylogenies are congruent. At the interspecific level (8 species of primates: 54 individuals), we analyzed the sequence polymorphism and divergence of each orthologous locus for both the flanking sequence and the microsatellite. The results showed a lower divergence of flanking sequences than expected in noncoding DNA and a relative stability of the first nucleotides close to the microsatellite. The location of each CAIII locus in a Low Copy Repeated element containing duplicated VCX/Y genes (approximately 1 kb) suggested that direct or indirect selection could explain these results. Moreover, the substitution rates in the flanking sequences and in the microsatellites were correlated. Thus, the evolutionary dynamics of microsatellites seems closely linked to the variation of spontaneous mutations in the surrounding regions.

Animals↗

PubMed1983

Aberrant replication of chromosomal DNA segments in CHO cells as a manifestation of a DNA repair system.

We have previously demonstrated that transient blocking of DNA synthesis with drugs such as 1-beta-D-arabinofuranosylcytosine results in some segments of the chromosomal DNA being replicated more than once in a single cell cycle. One explanation for this phenomenon might be that it is due to a perturbation of the cellular mechanism which normally controls the process of initiating replication of the chromosomal DNA and which ensures that each DNA segment is normally replicated once only in each cell cycle. To examine an alternative explanation, we have used the Chinese hamster ovary CHO-K1 cell line to test whether UV irradiation induces aberrant double replication of chromosomal DNA segments. We present data which show that UV irradiation induces a linear increase (regression coefficient, 0.996) in aberrant reinitiation of DNA replication in DNA segments replicated earlier in the same cell cycle. This was shown by DNA strands labelled with bromodeoxyuridine (BrdU) being synthesized off 3H-labelled template strands which were themselves synthesized during a [3H]thymidine pulse shortly before the UV irradiation. We suggest that blocked replication forks trigger an emergency response to unreplicated DNA segments in which abnormal origins of replication are used to circumvent this damage. This results in abnormal patterns of DNA replication, and it occurs whether DNA replication forks are blocked metabolically (such as with an inhibitor of DNA polymerase) or physically (as in the case of pyrimidine dimers).

Animals↗

PubMed1991

[Segments of Djungarian hamster chromosomes, specific for translocation of integration of amplified mdr1 genes, do not possess increased instability].

Earlier we have revealed in Djungarian hamster DM-15 cells three chromosomal segments (2p22, 5p1, 7q23-25) that are specific for transposition of amplified mdr1 genes from the site of location of resident gene copy (it was mapped to 4q21-23). In situ hybridization revealed in wild type cells no mdr1 homologous sequences in all these three segments. In this work we studied distribution of chromosomal breakages induced in DM-15 cells by aphidicolin, 5-fluorodeoxyuridine or N-phosphonacetyl-L-aspartate. The data obtained indicate that two of above mentioned segments. 2p22 and 7q23-25, contain no fragile sites. So, specificity of these segments for the transposition of amplified mdr1 genes is not due to their particular instability or to the presence in them of sequences homologous to amplifiable selectable gene.

Animals↗

PubMed1982

Joining of immunoglobulin heavy chain gene segments: implications from a chromosome with evidence of three D-JH fusions.

A chromosomal segment with a unique structure around the immunoglobulin heavy chain joining region (JH) has been molecularly cloned from an Abelson murine leukemia virus-transformed cell line. Attached to JH3 in the cloned DNA, in inverted sequence, is the DNA from JH1 to the JH2 recognition sequence. The inverted segment is attached at its other end to the 5' recognition sequence of a diversity segment (D). To form this structure, three joining events must have occurred on the same chromosome. One of these events could have been a normal D-JH joining but the others must have been irregular events including ones that result in inversions. One of the joining events left fused recognition elements from JH2 and a D whose sequence shows that, during joining, reciprocal joinings of the recognition elements must occur to fuse the heptameric elements back to back. Because joined D and JH undergo deletion of terminal coding sequence during recombination but the joined heptameric recognition sequences do not contain the deleted sequence, joining must be a nonreciprocal event. Also, extra nucleotides are inserted between D and JH as part of the joining process; it is suggested that this added sequence is a product of the activity of terminal deoxynucleotidyltransferase at the D/JH (and probably the VH/D) joints and that it represents a new element of heavy chain gene structure, the N region.

Animals↗