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Query: UNIPROT:P06889 (Mol)
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To improve DNA resolution of fluorescence in situ hybridization we have adapted a nuclear extraction technique, resulting in highly extended DNA loops arranged around the nuclear matrix in a halo-like structure. In situ hybridization signals from alphoid and cosmid DNAs appear as beads-on-a-string, which, according to preliminary experiments, results from the association of individual probe fragments. By multicolor hybridizations we have been able to determine relative map position and to easily detect 10 kb overlap between individual cosmid clones, each of which shows linear beaded signals of ca. 10 microns, suggesting that the DNA is essentially linearized in our protocol. The map configuration can be typically derived from analysis of 5-10 cells only. The resolution range of the technique is at least 10-200 kb, and probably as little as a few kb, thus greatly extending the abilities of the existing FISH methodologies. This novel technique is much more efficient and practicable than pronuclei hybridizations, another method for high resolution FISH, and readily produces results with probes of a variety of genomic origin. In conclusion the DNA halo technique should be able to contribute significantly to the assessment of cosmid and YAC overlaps as well as to the sizing of gaps between adjacent contigs generated in genome projects.
Hum Mol Genet 1992 Nov
PMID:High-resolution in situ hybridization using DNA halo preparations. 130 Nov 67

In the mammalian nervous system, serotonin (5-hydroxytryptamine) binds to distinct cell surface receptor subtypes that are defined by their ligand binding and effector-coupling properties. The 5HT1c receptor is a G-protein coupled receptor that stimulates phospholipase C-catalyzed hydrolysis of phosphatidylinositol bisphosphate, leading to the mobilization of intracellular calcium and to the activation of protein kinase C. By using somatic cell hybrid analysis and FISH, we have mapped the HTR1C locus to the human X chromosome, band q24 and to the mouse X chromosome region D-F4. Comparison of these map positions offers new insights into the evolution of human and murine X chromosomes. Since HTR1C is expressed in certain parts of the central nervous system and abnormal function of the serotoninergic system has been implicated in affective disorders, obsessive-compulsive disorder and epilepsy, establishing the precise map position of HTR1C is an important first step toward evaluating this locus as a candidate for mutations in these syndromes and in X-linked mental disorders.
Hum Mol Genet 1992 Dec
PMID:Serotonin receptor 1c gene assigned to X chromosome in human (band q24) and mouse (bands D-F4). 130 5

Since the technique of PCR was developed in 1985 (Saiki et al). many new forms of applications have been described in the literature. Of particular interest are PCR approaches, allowing amplification of unknown sequences. In this review these approaches are generally termed "Random PCR"s. While "conventional PCR" in the form that was first described by Saiki et al. is utilized for the amplification and subsequent detection of specific DNA sequences, which are precisely characterized in length and sequence, Random PCR is either used for universal amplification of prevailing DNA or for amplification of unknown intervening sequences which are not generally defined in length or sequence. We depict criteria for discrimination between conventional PCR and Random PCR. Furthermore, we have compiled a classification system for Random PCR approaches based on differentiation by primer structure (degenerate--non-degenerate). According to this classification system a general overview of published Random PCR approaches is given. Future aspects of application of Random PCR are mentioned and commented. Own investigations, combining Random PCR with the technique of chromosome microdissection and thus allowing characterization of unknown chromosomes or chromosome fragments via FISH, are presented. Results are briefly summarized.
Cell Mol Biol (Noisy-le-grand) 1995 Jul
PMID:Applications of random PCR. 758 Aug 45

Heat shock proteins (HSP) belong to a family of highly homologous proteins that are encoded by several genes and function as protein chaperones. A number of HSP genes have been described in the major histocompatibility complex (MHC) on chromosome 6. We have cloned and mapped one chromosome 14 HSP gene (HSPA2) using a genomic probe (pH2.3) derived from one of the HSP genes present in the MHC, which was previously shown to also detect sequences on chromosome 14. Screening of a chromosome 14-specific cosmid library yielded one relevant clone that contains an HSP-like sequence, showing a high degree of identity with the HSP genes from the MHC and with HSP70.2 (Hspa2) in the mouse. This new HSP gene is expressed abundantly in muscle, heart, oesophagus and brain, and to a lesser extent in testis. Its localization to 14q22 was established by using a somatic cell hybrid panel and FISH analysis. A pentanucleotide repeat motif, showing seven alleles, was also identified in the cosmid clone.
Hum Mol Genet 1994 Oct
PMID:A heat shock gene at 14q22: mapping and expression. 784 6

Autosomal fragile sites, unlike their X-linked counterparts, are not known to be associated with disease. However, one case report has highlighted a possible relationship between the inheritance of a rare folate-sensitive fragile site in band 11q23.3 (FRA11B) and the chromosome 11q23-->qter deletion in Jacobsen (11q-) syndrome. The mother and brother of the reported Jacobsen syndrome child are FRA11B carriers, suggesting that in vivo breakage at the fragile site during early development could have given rise to the chromosome deletion. We have tested this hypothesis by high resolution physical mapping of FRA11B and of the deletion chromosome breakpoint in the Jacobsen syndrome patient. A detailed restriction map of 600 kb of human chromosome band 11q23.3 has been assembled which covers the PBGD, CBL2 and THY1 genes. FISH experiments with YACs and cosmids from this region have localised FRA11B to an interval of approximately 100 kb containing the 5' end of the CBL2 gene, which includes a CCG trinucleotide repeat. This class of repeat is expanded in the four cloned examples of fragile site and therefore the CBL2 repeat is a candidate for the location of FRA11B. Further, it is shown that the chromosomal deletion breakpoint of the Jacobsen syndrome child maps within the same interval as the fragile site. The breakpoint has apparently been repaired and stabilised by the de novo addition of a telomere. These data are consistent with a role for an inherited fragile site in the aetiology of a chromosome deletion syndrome.
Hum Mol Genet 1994 Dec
PMID:Physical linkage of the fragile site FRA11B and a Jacobsen syndrome chromosome deletion breakpoint in 11q23.3. 788 8

The long-range organization of alphoid DNA arrays of human chromosome 21 was investigated using a mouse-human somatic cell hybrid. Two distinct long alphoid DNA arrays, the loci alpha 21-I and alpha 21-II, were identified in the centromere region of human chromosome 21. The alpha 21-I locus, composed of an array of 11 monomer repeat units (the 11 mer), was estimated to have a total length of 1.3 Mbp. CENP-B boxes, the binding sites of the centromere protein B (CENP-B), appeared in every other monomer unit in the 11 mer except for one place where two monomer units were repeated without any CENP-B box. The other locus, alpha 21-II, was found to be composed of alphoid subfamilies with low homology to the components of alpha 21-I locus. Five different alphoid clones presenting 32 monomer units in total were isolated from the alpha 21-II locus. Sequences of these monomer units diverged between 71-89% and no unit containing a CENP-B box was found. By analysis using two color FISH, the alpha 21-I was localized to the primary constriction, whereas the alpha 21-II site was located slightly to the short arm side. Furthermore, a combination of FISH and immunofluorescent staining indicated that the alpha 21-I site was co-localized and overlapped with the CREST centromere antigenic site on mitotic chromosomes and in interphase nuclei, while alpha 21-II was distributed broadly. Our data suggest that the locus alpha 21-I containing regularly spaced CENP-B boxes at high-frequency and the assembly site of the centromere antigens may be involved in common centromere function in both human and mouse cells.
Hum Mol Genet 1994 Aug
PMID:Distribution of CENP-B boxes reflected in CREST centromere antigenic sites on long-range alpha-satellite DNA arrays of human chromosome 21. 798 98

Free DNA was prepared from routinely harvested and fixed cells for high resolution FISH mapping using either a sodium hydroxide/ethanol mixture or 70% formamide. Hybridization signals from cosmid probes appeared as extended lines. The average length of signals on DNA prepared with sodium hydroxide was significantly greater than with formamide. A set of overlapping cosmids from the HLA class II region was used to determine how precisely the actual overlap or gap between probes can be calculated from the measured overlap or gap between their signals. Lengths of the probe signals and their known kilobase lengths were used as an internal ruler. The mean values calculated from the measured length from 30 or more signals for each probe pair showed remarkable conformity with the known kilobase lengths of their overlaps and gaps. Immediately adjacent probes could also be ordered on the released DNA. These simple procedures dramatically increase the speed with which relationships between probes can be determined during contig construction.
Hum Mol Genet 1994 Aug
PMID:Released chromatin: linearized DNA for high resolution fluorescence in situ hybridization. 798 2

The sequence of the tandem repeat sequence (D4Z4) associated with facioscapulohumeral muscular dystrophy (FSHD) has been determined: each copy of the 3.3 kb repeat contains two homeoboxes and two previously described repetitive sequences, LSau and a GC-rich low copy repeat designated hhspm3. By Southern blotting, FISH and isolation of cDNA and genomic clones we show that there are repeat sequences similar to D4Z4 at other locations in the human genome. Southern blot analysis of primate genomic DNA indicates that the copy number of D4Z4-like repeats has increased markedly within the last 25 million years. Two cDNA clones were isolated and found to contain stop codons and frameshifts within the homeodomains. An STS was produced to the cDNAs and analysis of a somatic cell hybrid panel suggests they map to chromosome 14. No cDNA clones mapping to the chromosome 4q35 D4Z4 repeats have been identified, although the possibility that they encode a protein cannot be ruled out. Although D4Z4 may not encode a protein, there is an association between deletions within this locus and FSHD. The D4Z4 repeats contain LSau repeats and are adjacent to 68 bp Sau3A repeats. Both of these sequences are associated with heterochromatic regions of DNA, regions known to be involved in the phenomenon of position effect variegation. We postulate that deletion of D4Z4 sequences could produce a position effect.
Hum Mol Genet 1994 Aug
PMID:Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy. 798 4

The chromosomal translocation (X;18)(p11.2;q11.2) represents the cytogenetic hallmark of human synovial sarcomas. Two related but distinct breakpoints within band Xp11.2 were reported previously by us and others using breakpoint-spanning YACs in conjunction with FISH. Interestingly, we found that the occurrence of these alternative breakpoints corresponds to the presence of different histologic characteristics of the tumors involved. Here we report the isolation, via subcloning of one of our YAC-derived cosmids, of probes which specifically hybridize to altered restriction fragments in tumor DNAs as compared to normal controls. By using a synovial sarcoma-derived der(X) containing somatic cell hybrid, which exhibits the more distal breakpoint, one of these aberrantly hybridizing fragments could be isolated via preparative gel electrophoresis. This fragment appears to contain chromosome X- and 18-derived sequences, as revealed by both FISH on normal metaphase spreads and Southern blot analysis of X- and 18-only somatic cell hybrids. We conclude that this genomic fragment is chimaeric in nature and contains the translocation breakpoint region. In addition, our results indicate that, in contrast to our findings on the X chromosome, a single locus on chromosome 18 may be involved in the development of different (sub)types of synovial sarcoma.
Hum Mol Genet 1994 May
PMID:Molecular cloning of the synovial sarcoma-specific translocation (X;18)(p11.2;q11.2) breakpoint. 808 61

RFLP typing of members of a neurofibromatosis type 2 (NF2) family suggested that affected individuals were hemizygous at the neurofilament heavy chain (NEFH) locus, possibly as a result of a disease-associated deletion. Conventional karyotyping revealed no evidence for a deletion and all or a majority of the affected family members were heterozygous for closely linked markers which mapped proximal to the NEFH locus (D22S1 and D22S56) and for the distal marker D22S32. FISH analysis confirmed a disease-associated germinal deletion on 22q which encompassed the NEFH locus, which is known to be very closely linked to NF2, but did not extend as far as the proximal Ewing sarcoma region or the distal leukaemia factor (LIF) locus. PFGE analysis with a LIF cosmid subclone identified patient-specific NotI and MluI fragments and suggested that the deletion is about 700 kb in length. Although this large deletion could be expected to eliminate a considerable fraction, and possibly all of the NF2 gene, the resulting phenotype is the mild, so-called Gardner subtype of NF2. The deletion should provide a useful mapping resource for characterising the chromosomal region containing the NF2 locus.
Hum Mol Genet 1993 Jun
PMID:A disease-associated germline deletion maps the type 2 neurofibromatosis (NF2) gene between the Ewing sarcoma region and the leukaemia inhibitory factor locus. 810 69


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