Showing papers on "Chromosome 22 published in 1992"

Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours

Abstract: Ewing's sarcoma and related subtypes of primitive neuroectodermal tumours share a recurrent and specific t(11;22) (q24;q12) chromosome translocation, the breakpoints of which have recently been cloned. Phylogenetically conserved restriction fragments in the vicinity of EWSR1 and EWSR2, the genomic regions where the breakpoints of chromosome 22 and chromosome 11 are, respectively, have allowed identification of transcribed sequences from these regions and has indicated that a hybrid transcript might be generated by the translocation. Here we use these fragments to screen human complementary DNA libraries to show that the translocation alters the open reading frame of an expressed gene on chromosome 22 gene by substituting a sequence encoding a putative RNA-binding domain for that of the DNA-binding domain of the human homologue of murine Fli-1.

The complete DNA sequence of yeast chromosome III.

Abstract: The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

Cytogenetic analysis by chromosome painting using dop-pcr amplified flow-sorted chromosomes

Abstract: A novel polymerase chain reaction (PCR) technique has been combined with chromosome flow sorting to characterise two lymphoblastoid cell lines and one medullary thyroid carcinoma cell line carrying translocations close to the locus for multiple endocrine neoplasia type 2A (MEN 2A). Five hundred copies of the derivative chromosome(s) were flow sorted from each cell line and amplified by degenerate oligonucleotide-primed-polymerase chain reaction (DOP-PCR). This generated pools of DNA sequences corresponding to the abnormal chromosomes, which were then used as probes in fluorescence in situ hybridisation (FISH) experiments on normal metaphase cells. The resultant chromosome paints revealed the portions of the normal chromosomes related to those involved in the translocations. By this technique, translocation breakpoints in bands p15, q11.2, and q21 of chromosome 10 were defined in the above cell lines, in two cases refining previous cytogenetic data. This study shows that flow sorting of aberrant chromosomes and chromosome painting can be used as a rapid aid to cytogenetic analysis, particularly in cases of difficult karyotypes, such as tumours. Furthermore, the DOP-PCR technique described here will have applications to other areas of genome analysis, such as cloning of new markers; its design will allow a general and representative amplification to occur from any starting DNA in any species.

The human Y chromosome: a 43-interval map based on naturally occurring deletions.

Abstract: A deletion map of the human Y chromosome was constructed by testing 96 individuals with partial Y chromosomes for the presence or absence of many DNA loci. The individuals studied included XX males, XY females, and persons in whom chromosome banding had revealed translocated, deleted, isodicentric, or ring Y chromosomes. Most of the 132 Y chromosomal loci mapped were sequence-tagged sites, detected by means of the polymerase chain reaction. These studies resolved the euchromatic region (short arm, centromere, and proximal long arm) of the Y chromosome into 43 ordered intervals, all defined by naturally occurring chromosomal breakpoints and averaging less than 800 kilobases in length. This deletion map should be useful in identifying Y chromosomal genes, in exploring the origin of chromosomal disorders, and in tracing the evolution of the Y chromosome.

A genetic etiology for DiGeorge syndrome: consistent deletions and microdeletions of 22q11.

Abstract: DiGeorge syndrome (DGS), a developmental field defect of the third and fourth pharyngeal pouches, is characterized by aplasia or hypoplasia of the thymus and parathyroid glands and by conotruncal cardiac malformations Cytogenetic studies support the presence of a DGS critical region in band 22q11 In the present study, we report the results of clinical, cytogenetic, and molecular studies of 14 patients with DGS Chromosome analysis, utilizing high-resolution banding techniques, detected interstitial deletions in five probands and was inconclusive for a deletion in three probands The remaining six patients had normal karyotypes In contrast, molecular analysis detected DNA deletions in all 14 probands Two of 10 loci tested, D22S75 and D22S259, are deleted in all 14 patients A third locus, D22S66, is deleted in the eight DGS probands tested Physical mapping using somatic cell hybrids places D22S66 between D22S75 and D22S259, suggesting that it should be deleted in the remaining six cases Parent-of-origin studies were performed in five families Four probands failed to inherit a maternal allele, and one failed to inherit a paternal allele On the basis of these families, and of six maternally and five paternally derived unbalanced-translocation DGS probands in the literature, parent of origin or imprinting does not appear to play an important role in the pathogenesis of DGS Deletion of the same three loci in all 14 DGS probands begins to delineate the region of chromosome 22 critical for DGS and confirms the hypothesis that submicroscopic deletions of 22q11 are etiologic in the vast majority of cases

The human Y chromosome: overlapping DNA clones spanning the euchromatic region

Abstract: The human Y chromosome was physically mapped by assembling 196 recombinant DNA clones, each containing a segment of the chromosome, into a single overlapping array. This array included more than 98 percent of the euchromatic portion of the Y chromosome. First, a library of yeast artificial chromosome (YAC) clones was prepared from the genomic DNA of a human XYYYY male. The library was screened to identify clones containing 160 sequence-tagged sites and the map was then constructed from this information. In all, 207 Y-chromosomal DNA loci were assigned to 127 ordered intervals on the basis of their presence or absence in the YAC's, yielding ordered landmarks at an average spacing of 220 kilobases across the euchromatic region. The map reveals that Y-chromosomal genes are scattered among a patchwork of X-homologous, Y-specific repetitive, and single-copy DNA sequences. This map of overlapping clones and ordered, densely spaced markers should accelerate studies of the chromosome.

Continuum of overlapping clones spanning the entire human chromosome 21q.

Abstract: A continuous array of overlapping clones covering the entire human chromosome 21q was constructed from human yeast artificial chromosome libraries using sequence-tagged sites as landmarks specifically detected by polymerase chain reaction. The yeast artificial chromosome contiguous unit starts with pericentromeric and ends with subtelomeric loci of 21q. The resulting order of sequence-tagged sites is consistent with other physical and genetic mapping data. This set of overlapping clones will promote our knowledge of the structure of this chromosome and the function of its genes.

Peripheral myelin protein–22 gene maps in the duplication in chromosome 17p11.2 associated with Charcot–Marie–Tooth 1A

Abstract: Charcot–Marie–Tooth disease 1A (CMT1A) is a hereditary demyelinating peripheral neuropathy, associated with a DNA duplication on chromosome 17p11.2. A related disorder in the mouse, trembler (Tr), maps to mouse chromosome 11 which has syntenic homology to human chromosome 17p. Recently, the peripheral myelin protein–22 (pmp–22) gene was identified as the likely Tr locus. We have constructed a partial yeast artificial chromosome contig spanning the CMT1A gene region and mapped the PMP–22 gene to the duplicated region. These observations further implicate PMP–22 as a candidate gene for CMT1A, and suggest that over–expression of this gene may be one mechanism that produces the CMT1A phenotype.

Cloning and characterization of the Ewing's sarcoma and peripheral neuroepithelioma t(11;22) translocation breakpoints.

Abstract: Ewing's sarcoma (ES) and peripheral neuroepithelioma (PN) are related tumors, possibly of neural crest origin, which are cytogenetically characterized by the specific translocation t(11;22)(q24;q 12). The cos5 locus, previously identified in the vicinity of the chromosome 22 breakpoint of this translocation, was shown by in situ hybridization on interphase nuclei to lie between VIIIF2 and LIF, two loci located on either side of the breakpoint and at a distance of less than 2,000 kb. The progressive expansion of this locus by chromosome walking led to the construction of a 300 kb contig, which finally crossed the breakpoint. The subsequent cloning of the two translocation junction fragments of a PN, followed by the molecular characterization of the translocation breakpoints of 20 ES and PN, showed that most chromosome 22 breakpoints are clustered within a small, 2 kb region. In contrast, the chromosome 11 breakpoints are scattered over a region of at least 40 kb. The translocation leads to the synthesis of a chimeric transcript that links sequences from chromosomes 22 and 11. Finally, no evidence was found of any specific difference in the position of ES and PN translocation breakpoints.

Genomic in situ hybridization to identify alien chromosomes and chromosome segments in wheat.

Abstract: Genomic in situ hybridization was used to identify alien chromatin in chromosome spreads of wheat, Triticum aestivum L., lines incorporating chromosomes from Leymus multicaulis (Kar. and Kir.) Tzvelev and Thinopyrum bessarabicum (Savul. and Rayss) Love, and chromosome arms from Hordeum chilense Roem. and Schult, H. vulgare L. and Secale cereale L. Total genomic DNA from the introgressed alien species was used as a probe, together with excess amounts of unlabelled blocking DNA from wheat, for DNA:DNA in-situ hybridization. The method labelled the alien chromatin yellow-green, while the wheat chromosomes showed only the orange-red fluorescence of the DNA counterstain. Nuclei were screened from seedling root-tips (including those from half-grains) and anther wall tissue. The genomic probing method identified alien chromosomes and chromosome arms and allowed counting in nuclei at all stages of the cell cycle, so complete metaphases were not needed. At prophase or interphase, two labelled domains were visible in most nuclei from disomic lines, while only one labelled domain was visible in monosomic lines. At metaphase, direct visualization of the morphology of the alien chromosome or chromosome segment was possible and allowed identification of the relationship of the alien chromatin to the wheat chromosomes. The genomic in-situ hybridization method is fast, sensitive, accurate and informative. Hence it is likely to be of great value for both cytogenetic analysis and in plant breeding programmes.

A novel reciprocal chromosome translocation t(11;22)(p13;q12) in an intraabdominal desmoplastic small round-cell tumor.

Abstract: We report an intraabdominal desmoplastic small round-cell tumor that contains a novel reciprocal chromosome translocation t(11;22)(p13;q12). The tumor showed a reciprocal chromosome translocation which is different from the (11;22)(q24;q12) translocations seen in Ewing's and other small-cell tumors but affects the same break-point on chromosome 22(q12). This reciprocal chromosome translocation may prove to be a marker for intraabdominal desmoplastic small round-cell tumors.

Reverse chromosome painting: a method for the rapid analysis of aberrant chromosomes in clinical cytogenetics.

Abstract: We describe a method, termed reverse chromosome painting, which allows the rapid analysis of the content and breakpoints of aberrant chromosomes. The method involves the sorting of small numbers of the aberrant chromosome from short term blood culture preparations or cell lines by using bivariate flow karyotype analysis. The sorted chromosomes are amplified and biotin labelled enzymatically using a degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), the product annealed to metaphase spreads from normal subjects, and hybridisation detected using fluorescence in situ hybridisation (FISH). We show the usefulness of this method for routine clinical cytogenetics by the analysis of cases involving an insertion, a deletion, a translocation, and two cases of a chromosome with additional material of unknown origin. The method has particular application for the rapid resolution of the origin of de novo unbalanced chromosome duplications.

Homologies in human and Macaca fuscata chromosomes revealed by in situ suppression hybridization with human chromosome specific DNA libraries.

Abstract: We established chromosomal homologies between all chromosomes of the human karyotype and that of an old world monkey (Macaca fuscata) by chromosomal in situ suppression (CISS) hybridization with human chromosome specific DNA libraries. Except for the human chromosome 2 library and limited cross-hybridization of X and Y chromosome libraries all human DNA libraries hybridized to single GTG-banded macaque chromosomes. Only three macaque chromosomes (2, 7, 13) were each hybridized by two separate human libraries (7 and 21, 14 and 15, 20 and 22 respectively). Thus, an unequivocally high degree of synteny between human and macaque chromosomes has been maintained for more than 20 million years. As previously suggested, both Papionini (macaques, baboons, mandrills and cercocebus monkeys, all of which have nearly identical karyotypes) and humans are chromosomally conservative. The results suggest, that CISS hybridization can be expected to become an indispensable tool in comparative chromosome and gene mapping and will help clarify chromosomal phylogenies with speed and accuracy.

Cytogenetic and loss of heterozygosity studies in ependymomas, pilocytic astrocytomas, and oligodendrogliomas.

Abstract: Cytogenetic and/or loss of heterozygosity studies were performed on 13 ependymomas, 11 pilocytic astrocytomas, and 18 oligodendrogliomas. Loss of chromosome 22 was the most frequent genetic abnormality among the ependymomas. We found no consistent genetic abnormality in pilocytic astrocytomas. The most common genetic abnormality in oligodendrogliomas was loss of a portion of chromosome 19. Each informative oligodendroglioma had loss of alleles mapped to the long arm (q) of chromosome 19. One oligodendroglioma had an apparent homozygous deletion of the D19S8 locus. Our results, when combined with those in the literature, indicate that chromosomes 9, 11, and 22 may harbor genes important for the pathogenesis of ependymomas and that 19q probably harbors a gene important for the pathogenesis of oligodendrogliomas.

Degenerating Y chromosome of Drosophila miranda: a trap for retrotransposons.

Abstract: In Drosophila miranda, the larval cuticle protein (Lcp) genes are located on the X2 and Y chromosomes, while in other Drosophila species the Lcp genes are inherited on the autosomes. We chose the D. miranda species as a model system to analyze the molecular bases of Y chromosome degeneration, a phenomenon observed in many species. DNA sequence analysis of the Y chromosomal Lcp gene locus reveals dense clustering of trapped retrotransposons. Once inserted at the Y chromosomal location they cannot easily be eliminated by unequal crossing-over, as recombination is a rare event in Drosophila males. In addition, we have uncovered an example of a completely inactive allele on the degenerating Y chromosome. The existence of such inactive Y-specific alleles was originally predicted in H. J. Muller9s model for Y chromosome degeneration. We demonstrate that the Y chromosomal Lcp4 allele is no longer transcribed. From the divergence in DNA sequence organization of former homologous chromosome regions we conclude that changes in chromosome structure and destruction of genetic activity in degenerating Y chromosomes are based on one major mechanism, which operates by means of transposable elements.

Molecular cytogenetic and clinical studies of 42 patients with marker chromosomes.

Abstract: The molecular cytogenetic characterization and clinical details of 20 patients with marker chromosomes are presented. These 20 patients, together with another 22 patients previously published, represent a cohort in which the chromosomal origin of the marker chromosomes was successfully determined in all but one case. Examination of the pooled data suggests that the satellited markers derived from chromosomes 14, 15 (when metacentric or submetacentric), those whose origin is either 13 or 21, and those small ring autosomal markers derived from both alphoid and satellite II or III pericentric hetero-chromatin of chromosomes 1, 9, 15, and 16 are all associated with a low risk of phenotypic abnormality. The markers identified as i(18p), ring chromosomes derived from various autosomes, and satellited markers derived from chromosome 22 are associated with a high risk of phenotypic abnormality. The phenotype of patients with acrocentric markers derived from chromosome 15 was equivocal, perhaps as a result of imprinting. Additional data are required to confirm these trends. The mild mental retardation and abnormal face of a patient with a small ring chromosome derived from chromosome 4 are described. Identification of patients with small rings originating from particular chromosomes may allow the recognition of new syndromes. © 1992 Wiley-Liss, Inc.

The presence of interstitial telomeric sequences in constitutional chromosome abnormalities.

Abstract: We describe a novel chromosome structure in which telomeric sequences are present interstitially, at the apparent breakpoint junctions of structurally abnormal chromosomes. In the linear chromosomes with interstitial telomeric sequences, there were three sites of hybridization of the telomere consensus sequence within each derived chromosome: one at each terminus and one at the breakpoint junction. Telomeric sequences also were observed within a ring chromosome. The rearrangements examined were constitutional chromosome abnormalities with a breakpoint assigned to a terminal band. In each case (with the exception of the ring chromosome), an acentric segment of one chromosome was joined to the terminus of an apparently intact recipient chromosome. One case exhibited apparent instability of the chromosome rearrangement, resulting in somatic mosaicism. The rearrangements described here differ from the telomeric associations observed in certain tumors, which appear to represent end-to-end fusion of two or more intact chromosomes. The observed interstitial telomeric sequences appear to represent nonfunctional chromosomal elements, analogous to the inactivated centromeres observed in dicentric chromosomes.

Organization and nucleotide sequence of the human KIT (mast/stem cell growth factor receptor) proto-oncogene.

Abstract: We have cloned and sequenced the human KIT proto-oncogene, which contains 21 exons and spans more than 34 kb of DNA on chromosome segment 4q12. We also establish physical linkage between the KIT gene and the related PDGFRA gene. The organization of the KIT gene is virtually identical to that of the homologous FMS gene, located on chromosome 5. Together, these data suggest that the KIT and PDGFRA genes on chromosome 4 and the FMS and PDGFRB genes on chromosome 5 arose by duplication of a common ancestral gene, followed by duplication of a chromosome.

Meiotic chromosome condensation and pairing in Saccharomyces cerevisiae studied by chromosome painting.

Abstract: Non-isotopic high resolution in sity hybridization was applied to cytological preparations of sporulating yeast cells. Ribosomal DNA (rDNA) and chromosome V-specific recombinant lambda clones were used to tag individual chromosomes and chromosome subregions. This allowed the study of chromosome behaviour during early meiotic prophase. It was found that chromatin becomes condensed and homologous DNA sequences then appear to become aligned prior to synaptonemal complex formation.

Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3

Abstract: A total of 116,118 basepairs (bp) derived from three cosmids spanning the ERCC1 locus of human chromosome 19q13.3 have been sequenced with automated fluorescence-based sequencers and analysed by polymerase chain reaction amplification and computer methods. The assembled sequence forms two contigs totalling 105,831 bp, which contain a human fosB proto-oncogene, a gene encoding a protein phosphatase, two genes of unknown function and the previously-characterized ERCC1 DNA repair gene. This light band region has a high average density of 1.4 Alu repeats per kilobase. Human chromosome light bands could therefore contain up to 75,000 genes and 1.5 million Alu repeats.

A prospective cytogenetic study of 36 cases of DiGeorge syndrome.

Abstract: Cytogenetic analysis was carried out in a prospective series of 36 children with DiGeorge syndrome. High-resolution banding (> 850 bands/haploid set) was achieved in 30 cases. Monosomy 22q11.21-->q11.23 was found in 9 of these 30 cases. In each of these cases monosomy 22q11.21-->q11.23 resulted from an interstitial deletion and not from a translocation. No other chromosome abnormalities were seen.

Loss of heterozygosity for distal markers on 22q in human gliomas

Abstract: Loss of constitutional heterozygosity as determined through the analysis of restriction-fragment-length polymorphism (RFLP) on tumoral and constitutional DNA has proven to be helpful to delimit the location of tumor-suppressor genes in the human genome. In malignant gliomas this approach indicates that chromosomes 9p, 10, 17p, and 22 may contain genes of this category involved in its origin and/or progression. Regarding chromosome 22, the data so far provided by molecular studies confirmed those previously reported by cytogenetic studies, suggesting the existence of a sub-group of malignant gliomas characterized by monosomy of this chromosome. However, the precise location of the putative glioma suppressor gene on chromosome 22 remains ambiguous. We have performed a combined cytogenetic and RFLP study on a series of 31 gliomas, looking for structural abnormalities of this chromosome. In 3 instances, terminal deletions of the long arm of chromosome 22 were observed by both methodologies, suggesting that the band q13 region distal to the D22S80 marker might be the critical domain non-randomly involved in tumor suppression of gliomas. © 1992 Wifey-Liss, Inc.

The human catechol-O-methyltransferase (COMT) gene maps to band q11.2 of chromosome 22 and shows a frequent RFLP with BglI.

Abstract: We have been able to assign the human catechol-O-methyltransferase gene (COMT) to chromosome 22q11.2 by using Southern blot analysis of panels of somatic cell hybrids and chromosomal in situ hybridization. Furthermore, Southern blot analysis of DNA from blood and bone marrow samples of a patient with chronic myeloid leukemia (CML), having an extra Philadelphia chromosome (Ph1) in addition to the one produced by the reciprocal translocation between chromosomes 9 and 22, showed increased COMT and BCR gene dosage as compared to DNAs originating from CML patients with only one Ph1 chromosome or from chromosomally normal individuals. Control hybridizations of the same blot with TCRG- and TCRA-specific probes showed corresponding signal intensities in all samples. A relatively frequent two-allele COMT gene RFLP (PIC = 0.37) was recognized in DNAs digested with BglI. Our gene mapping result is in concordance with that previously reported by Brahe et al. (1986), who used an autoradiozymogram assay on different somatic cell hybrids to map this gene to chromosome 22.

Isolation of chromosome 21-specific yeast artificial chromosomes from a total human genome library.

Abstract: A new approach for the isolation of chromosome–specific subsets from a human genomic yeast artificial chromosome (YAC) library is described. It is based on the hybridization with an Alu polymerase chain reaction (PCR) probe. We screened a 1.5 genome equivalent YAC library of megabase insert size with Alu PCR products amplified from hybrid cell lines containing human chromosome 21, and identified a subset of 63 clones representative of this chromosome. The majority of clones were assigned to chromosome 21 by the presence of specific STSs and in situ hybridization. Twenty–nine of 36 STSs that we tested were detected in the subset, and a contig spanning 20 centimorgans in the genetic map and containing 8 STSs in 4 YACs was identified. The proposed approach can greatly speed efforts to construct physical maps of the human genome.