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At least 1,189 records · Page 66Linked to original sources
PubMed1998

Isolation of yeast artificial chromosomes containing the entire transcriptional unit of the human FGF1 gene: a 720-kb contig spanning human chromosome 5q31.3-->q32.

The q31-q33 region of chromosome 5 includes a number of genes encoding growth factors, growth factor receptors, and hormone/neurotransmitter receptors. The human fibroblast growth factor 1 locus (FGF1) resides in this region of chromosome 5, which is frequently lost in myelodysplastic syndromes and acute myeloid leukemia patients. Other disease loci, including the loci for limb-girdle muscular dystrophy and an autosomal dominant deafness, have been mapped on this region, but their genes have not been isolated. It was shown that the critical region lost in two patients with the 5q- syndrome resides between FGF1 and IL12B. We previously reported the construction of a yeast artificial chromosome (YAC) contig spanning 330 kb around the FGF1 gene. Here we report the isolation of additional YAC clones that extend 290 kb from the previous contig. Sequence-tagged sites developed from the outermost YAC ends were utilized in the contig cloning of two P1 clones P1Y2 and P1Y8. Together, these YAC and P1 clones span 720 kb around the FGF1 locus. With the use of fluorescence in situ hybridization, a physical map has been constructed of these P1 and GRL (glucocorticoid receptor locus) probes on metaphase and interphase chromosomes. On the basis of our work and the known orientation of GRL transcription, the determined order of these loci on chromosome 5q31.3-q32 is centromere-P1Y8-3'[FGF1]5'-P1Y2-5'[GRL]3'-telome re. Knowing the transcriptional orientation of the FGF1 gene relative to the centromere will now facilitate the directional cloning of clinically important genes that may reside in this region.

Base Sequence↗
PubMed1998

A case of dermatofibrosarcoma protuberans with a ring chromosome 5 and a rearranged chromosome 22 containing amplified COL1A1 and PDGFB sequences.

Dermatofibrosarcoma protuberans (DFSP) is a cutaneous tumour of borderline malignancy, the cytogenetic features of which include the translocation t(17;22)(q22;q13) or, more commonly, supernumerary ring chromosomes containing material from 17q22 and 22q13. These rearrangements result in the COL1A1/PDGFB fusion gene. Here, we describe a case of DFSP displaying a ring chromosome 5 together with a large marker chromosome composed of chromosome 22 alphoid DNA, material from distal 12q and amplified COL1A1 and PDGFB sequences. This is the first case of DFSP with multiple copies of COL1A1 and PDGFB not confined to ring chromosomes, showing that DFSP is similar to other borderline malignant mesenchymal tumours, where rings and giant markers are alternative vehicles for amplified material.

Adolescent↗
PubMed1999

Cytogenetic alignment of the bovine chromosome 13 genome map by fluorescence in-situ hybridization of human chromosome 10 and 20 comparative markers.

A bovine bacterial artificial chromosome (BAC) library was screened for the presence of six genes (IL2RA, VIM, THBD, PLC-II, CSNK2A1 and TOP1) previously assigned to human chromosomes 10 or 20 (HSA10 or HSA20). Four of the genes were found represented in the bovine BAC library by at least one clone. The identified BAC clones were used as probes in single-color fluorescence in-situ hybridization (FISH) to determine the chromosomal band location of each gene. As predicted by the human/bovine comparative map and comparative chromosome painting analysis, the four genes mapped to bovine chromosome 13 (BTA13). Dual-color FISH was then used to integrate these four type I markers into the existing BTA13 genome map. These FISH results anchor the BTA13 genome map from bands 14-23, and confirm the presence of a conserved HSA10 homologous synteny group on BTA13 centromeric to a HSA20 homologous segment.

Animals↗
PubMed2003

Precise identification of chicken chromosomes in the lampbrush form using chromosome painting probes.

Chromosome painting probes specific for macrochromosomes 1, 2, 3, 4, 5, and Z were applied to both mitotic and lampbrush chromosomes of the chicken (Gallus gallus domesticus). Five autosomal macrobivalents and sex chromosome Z in the lampbrush phase were identified and their correspondence to the target chromosomes in the metaphase of mitosis was shown. Nascent transcripts on lateral loops of the target lampbrush chromosome were intensively labelled when the hybridization was performed without RNase A treatment according to the DNA/(DNA + RNA) hybridization protocol.

Animals↗
PubMed2005

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori.

In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed.

Animals↗
PubMed1996

Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure.

This study provides a three-dimensional (3D) analysis of differences between the 3D morphology of active and inactive human X interphase chromosomes (Xa and Xi territories). Chromosome territories were painted in formaldehyde-fixed, three-dimensionally intact human diploid female amniotic fluid cell nuclei (46, XX) with X-specific whole chromosome compositive probes. The colocalization of a 4,6-diamidino-2-phenylindole dihydrochloride-stained Barr body with one of the two painted X territories allowed the unequivocal discrimination of the inactive X from its active counterpart. Light optical serial sections were obtained with a confocal laser scanning microscope. 3D-reconstructed Xa territories revealed a flatter shape and exhibited a larger and more irregular surface when compared to the apparently smoother surface and rounder shape of Xi territories. The relationship between territory surface and volume was quantified by the determination of a dimensionless roundness factor (RF). RF and surface area measurements showed a highly significant difference between Xa and Xi territories (P < 0.001) in contrast to volume differences (P > 0.1). For comparison with an autosome of similar DNA content, chromosome 7 territories were additionally painted. The 3D morphology of the chromosome 7 territories was similar to the Xa territory but differed strongly from the Xi territory with respect to RF and surface area (P < 0.001).

Amniotic Fluid↗
PubMed2001

Characterization of a maize chromosome 4 centromeric sequence: evidence for an evolutionary relationship with the B chromosome centromere.

Previous work has identified sequences specific to the B chromosome that are a major component of the B centromere. To address the issue of the origin of the B and the evolution of centromere-localized sequences, DNA prepared from plants without B chromosomes was probed to seek evidence for related sequences. Clones were isolated from maize line B73 without B chromosomes by screening DNA at reduced stringency with a B centromeric probe. These clones were localized to maize centromere 4 using fluorescence in situ hybridization. They showed homology to a maize centromere-mapped sequence, to maize B chromosome centromere sequences, and to a portion of the unit repeat of knobs, which act as neocentromeres in maize. A representative copy was used to screen a BAC library to obtain these sequences in a larger context. Each of the six positive BACs obtained was analyzed to determine the nature of centromere 4-specific sequences present. Fifteen subclones of one BAC were sequenced and the organization of this chromosome 4-specific repeat was examined.

Base Sequence↗
PubMed1995

Definition of the blepharophimosis, ptosis, epicanthus inversus syndrome critical region at chromosome 3q23 based on the analysis of chromosomal anomalies.

Blepharophimosis syndrome (BPES) is an autosomal dominant disorder of craniofacial development, the features of which are small palpebral fissures (blepharophimosis), drooping eyelids (ptosis) and a skin fold arising from the lower eyelid (epicanthus inversus). The chromosomal localization and identity of the BPES locus is not known with certainty. In the current paper, DNA samples from three individuals with a clinical history of BPES, two with interstitial deletions (cases 1 and 2) and one with a balanced translocation (case 3) all involving chromosome 3q23, were analyzed. Allele loss studies using short tandem repeat markers in cases 1 and 2 suggested that the region between the markers D3S1292 and D3S1306 was deleted in both cases. Subsequently, the derived chromosomes resulting from the translocation in case 3 were segregated in interspecific somatic cell hybrids. Analysis of the resultant hybrids showed that D3S1615 was retained in the derived chromosome 3, whereas D3S1316 was retained in the derived chromosome 4. In neither case was the marker present in the reciprocal hybrid. These results indicate that the BPES critical region lies in the D3S1615-D3S1316 interval.

Abnormalities, Multiple↗
PubMed1997

Familial hypomagnesemia maps to chromosome 9q, not to the X chromosome: genetic linkage mapping and analysis of a balanced translocation breakpoint.

Familial hypomagnesemia with secondary hypocalcemia (HSH) (MIM 307600) was studied in three inbred Bedouin kindreds from Israel. The three kindreds, one extended and two nuclear families, contained 13 affected individuals, 11 males and two females. Assuming that the individuals affected with hypomagnesemia shared a chromosomal region inherited from a common ancestor, we used a DNA pooling strategy in a genome-wide search for loci which show homozygosity for shared alleles in affected individuals. DNA samples from affected individuals within a single kindred were pooled and used as the template for PCR amplification of short tandem repeat polymorphic markers (STRPs). Pooled DNA from unaffected siblings and parents were used as controls. A shift towards homozygosity was observed in the affected DNA pool compared with the control pools with D9S301 (GATA7D12). Genotyping of individual DNA samples with D9S301 and several flanking markers confirmed linkage to chromosome 9 with maximum LOD scores of 3.4 (theta = 0.05), 3.7 (theta = 0) and 2.3 (theta = 0) for the three families. We have identified a 14 cM interval on chromosome 9 (9q12-9q22.2), flanked by proximal marker D9S1874 and distal marker D9S1807, within which all affected individuals from the three kindreds are homozygous for a shared haplotype. The disease segregates with a common affected haplotype in the three families, suggesting that hypomagnesemia is caused by a common ancestral mutation in these families. Although HSH has been previously reported to be X linked, these linkage data demonstrate that the disorder is an autosomal recessive disease in these kindreds. Mapping of a chromosomal breakpoint in a somatic cell line established from a patient with HSH and a balanced X;9 translocation placed the chromosomal breakpoint in a 500 kb region flanked by D9S1844 and D9S273. Identification of the gene responsible for hypomagnesemia will provide insight into the regulation of this essential cation.

Arabs↗
PubMed2001

Meiotic behaviour of the sex chromosomes in three patients with sex chromosome anomalies (47,XXY, mosaic 46,XY/47,XXY and 47,XYY) assessed by fluorescence in-situ hybridization.

Meiotic studies using multicolour fluorescent in-situ hybridization (FISH) and chromosome painting were carried out in three patients with sex chromosome anomalies (47,XXY; 46,XY/47,XXY and 47,XYY). In the two patients with Klinefelter syndrome, although variable percentages of XXY cells (88.5 and 28.3%) could be found in the pre-meiotic stages, none of the abnormal cells entered meiosis, and all pachytenes were XY. However, the abnormal testicular environment of these patients probably resulted in meiotic I non-disjunction, and a certain proportion of post-reductional cells were XY (18.3 and 1.7%). The fact that none of the spermatozoa were XY also suggests the existence of an arrest at the secondary spermatocyte or the spermatid level. In the XYY patient, most (95.9%) premeiotic cells were XYY. The percentage of XYY pachytenes was 57.9%. The sex chromosomes were either in close proximity (XYY) or the X chromosome was separated from the two Ys (X + YY). A high proportion (42.1%) of post-reductional germ cells were XY. However, only 0.11% of spermatozoa were disomic for the sex chromosomes. In this case, the data suggest the existence of an arrest of the abnormal cells at the primary and the secondary spermatocyte or the spermatid level, giving rise to the continuous elimination of abnormal cells in the germ-cell line along spermatogenesis. The fact that the proportion of diploid spermatozoa was only increased in one of the three cases (XXY) is also suggestive of an arrest of the abnormal cell lines in these patients. The two apparently non-mosaic patients were, in fact, germ-cell mosaics. This suggests that the cytogenetic criteria used to define non-mosaic patients may be inadequate; thus, the risk of intracytoplasmic sperm injection in apparently non-mosaics may be lower than expected.

Adult↗
PubMed1996

Mapping of the 150 kb spoIIIC-pheA region of the Bacillus subtilis chromosome using Long Accurate PCR and three yeast artificial chromosomes.

We constructed a PCR map of the 150 kb spoIIIC-pheA region of the Bacillus subtilis chromosome. It was established using known sequences of the spoIIIC, blt, aadK, sacC, spoVB and pheA loci and eight random sequence tags. The tags were generated using PFGE-purified DNA of yeast artificial chromosome (YAC) 11-17 from the yeast clone which carries the major part of this region. The ends of two other YACs were positioned on the map using total DNA extracted from yeast cells carrying them. The procedure allowed the placement of precisely known and new (putative) genes on the physical chromosome map and the generation of sufficient amounts of DNA for sequencing this region. Apart from allowing correction of the genetic map in this region, these results demonstrate how a collection of long segments of bacterial chromosome and Long Accurate PCR can be used for reliable high-resolution physical mapping of an extended chromosome area.

Bacillus subtilis↗
PubMed1995

Molecular analysis of the chromosomal breakpoint and fusion transcripts in the acute lymphoblastic SEM cell line with chromosomal translocation t(4;11).

The chromosomal breakpoint and fusion transcripts of the pre-B-leukaemia-derived SEM cell line carrying a reciprocal t(4;11)(q21;q23) translocation were analysed. The breakpoint from derivative chromosome der4 was cloned and sequenced. The crossover site was localized in intron 7 of the ALL-1 gene on chromosome 11q23 and in a large intron of the AF-4 (FEL) gene. RNA transcripts from both wild-type genes and both hybrid genes were detected by reverse transcriptase polymerase chain reaction (RT-PCR) assays. In addition, alternatively spliced mRNA species derived from the der4 chromosome were found. They were generated by using the exon 5' of the breakpoint on der4 as a common splice donor site and the 5' boundaries of exons 8 or 9 of the ALL-1 gene as alternative splice acceptor sites. The hypothesis is proposed that selective pressure operators to maintain the presence of both derivative chromosomes as important elements in the leukaemogenic process.

Base Sequence↗
PubMed1996

Primed IN situ labelling (PRINS) as a rational procedure for identification of marker chromosomes using a panel of primers differentially tagging the human chromosomes.

PRimed IN Situ labelling (PRINS) is a highly specific and sensitive technique for detecting DNA sequences on human chromosomes in situ. PRINS is currently being introduced for research and routine analysis in clinical and cancer genetics. In this paper, we report a rational PRINS procedure for the rapid identification of marker chromosomes. Using this method it is possible to test a sample from a patient with up to eight different primers simultaneously on one slide. We have synthesized oligonucleotide primers that can differentially tag the human chromosomes, and with the protocol presented in this report we are able to identify the chromosomal origin of a marker chromosome within 2 hours.

Amniocentesis↗
PubMed2005

Stillborn baby with partial monosomy of the short arm of chromosome 5 and partial trisomy of the short arm of chromosome 20.

A stillborn baby with multiple malformations, including cardiac defects and cerebellar hypoplasia, is described. The abnormal features were ascribed to an unbalanced chromosome translocation, resulting in a partial deletion of the short arm of chromosome 5 and a partial trisomy of the short arm of chromosome 20. A parental balanced translocation t(5; 20)(p13.3; p11.23) was identified. The present case is the first case in Japan of monosomy of the short arm of chromosome 5 and trisomy of the short arm of chromosome 20.

Abnormalities, Multiple↗
PubMed2001

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes.

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.

Chromosomes↗
PubMed1998

Homologies between human and dolphin chromosomes detected by heterologous chromosome painting.

Human chromosome-specific probes for the entire karyotype were hybridized to metaphase spreads of the Atlantic bottlenose dolphin, Tursiops truncatus, to directly compare the evolutionary conservation of chromosomal segments between these two distantly related species. All human chromosomal paints, except the Y probe, hybridized to Tursiops counterparts, and every dolphin chromosome was painted except for the smallest submetacentric pair. In our analysis, 36 segments of conserved synteny common to the human and dolphin genomes were identified. The distribution of conserved chromosomal segments and the specific rearrangement patterns found between the two genomes are presented and discussed.

Animals↗
PubMed1998

Comparative cytogenetic mapping reveals chromosome rearrangements between the X chromosomes of two closely related mammalian species (cattle and goats).

Cytogenetic localization of 24 BACs containing type I (genes and ESTs) and type II (microsatellites) markers were used to construct cytogenetic maps of caprine (CHI) and bovine (BTA) X chromosomes. Comparison of these two maps revealed that the distal region of the goat X long arm (CHI Xq38-->q42) was located inside the bovine X chromosome, between PGK1 (BTA Xq25) and DVEPC137 (BTA Xq12). The marker order was globally conserved without any pericentric inversion, as previously postulated in the literature. The caprine centromere was found between DVEPC053 and DVEPC102 (belonging to the same band in the bovine X: BTA Xq41), whereas the bovine centromere was between DVEPC076 and DVEPC132, belonging to the same region of the caprine X chromosome (CHI Xq31-->q33). The pseudoautosomal region was situated at the tip of the bovine X long arm and on the tiny short arm of the caprine X chromosome. In the non-pseudoautosomal (NPA) region, the synteny of coding sequences was well conserved between the human species and the two ruminant species, but the gene order was dramatically divergent. It is suggested that the 24 BACs of this study could constitute a new tool to measure phylogenetic distances between different mammalian species by comparing chromosome rearrangements inside the NPA region of the X.

Animals↗
PubMed2001

Chromosome homologies between man and mountain zebra (Equus zebra hartmannae) and description of a new ancestral synteny involving sequences homologous to human chromosomes 4 and 8.

Using human chromosome painting probes, we looked for homologies between human and mountain zebra (Equus zebra hartmannae, Equidae, Perissodactyla) karyotypes. Except for two very short segments, all euchromatic regions were found to have a human homologous chromosome segment. Conserved syntenies previously described in various mammalian orders were detected. Each synteny corresponded to a chromosomal region homologous to two parts of human chromosomes: HSA3 and HSA21, HSA7 and HSA16, HSA12 and HSA22, and HSA16 and HSA19. Chromosomal segments homologous to a part of HSA11 and HSA19p are found syntenic in zebra, horse and donkey, suggesting that this group of synteny has been inherited from an Equidae or Perissodactyla common ancestor. A synteny of segments homologous to parts of HSA4 and HSA8 was observed in zebra and horse. It also exists in the rabbit (Lagomorpha) and several Carnivora species. A second group of taxa which does not have this region of synteny is composed of primates, Chiroptera and Insectivora, and possibly also Cetacea and Scandantia. Thus, the presence or absence of this region of synteny may separate two groups of eutherian mammals.

Animals↗