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At least 127 records · Page 7Linked to original sources
PubMed1987

Expression and rescuing of a cloned human tumour necrosis factor gene using an EBV-based shuttle cosmid vector.

A cosmid vector carrying the Epstein-Barr virus origin of replication, the EBNA-1 gene, the hygromycin phosphotransferase (hph) gene and pBR322 sequences has been constructed. This cosmid can replicate autonomously in the nucleus of human tissue culture cells, even when it carries a 35-kb long insert. The cosmid can be rescued from the transfected cells by cloning it directly into ampicillin-sensitive Escherichia coli. A gene for human tumour necrosis factor (TNF) cloned into this cosmid vector was introduced in tissue culture cells, where it was transcribed into mature mRNA.

Cell Line↗
PubMed1994

Physical mapping of chromosome 17 cosmids by fluorescence in situ hybridization and digital image analysis.

We used fluorescence in situ hybridization and digital image analysis to localize cosmids along human chromosome 17. Seventy-one cosmids were selected at random from a chromosome 17 library constructed from a partial Sau3AI digest of flow-sorted chromosomes from a mouse-human hybrid cell line. Sixty-three of these (89%) gave a signal only on chromosome 17. The 40 cosmids producing the most distinct hybridization signals in metaphase and interphase cells were precisely mapped using digital image analysis. An additional 20 cosmids, previously mapped by linkage analysis, were also mapped. The order of these probes determined by metaphase mapping was consistent with the order determined by linkage analysis.

Chromosome Mapping↗
PubMed1994

Isolation and regional localization of cosmid linking clones from human chromosome 12.

We have developed a new method for constructing cosmid linking libraries. The method is based on the insertion of a selection gene, beta-lactamase, in genomic cosmid clones containing recognition sites for rare-cutting enzymes. The selection gene is maintained as a gene cassette in a plasmid and may be excised by the enzymes NotI, SacII, SplI, MluI, BssHII, and NarI or combinations of these enzymes. Using this gene cassette and a genomic cosmid library made from a human-hamster cell line containing the human chromosome 12 as its only human component, a chromosome 12-specific NotI linking library was constructed. The NotI linking clones contained recognition sites for other rate-cutting enzymes, SacII and BssHII, at high frequency, indicating the presence of CpG islands. Thirty cosmid linking clones were regionally localized by FISH and were found to be clustered to chromosome bands 12p13, 12q13, and 12q24.

Animals↗
PubMed1996

A 900-kb cosmid contig and 10 new transcripts within the candidate region for myotubular myopathy (MTM1).

The X-linked myotubular myopathy locus (MTM1) has been assigned to the Xq28 region by linkage analysis. By observation of an interstitial deletion in a female patient, the candidate region could be further reduced to a region of 600 kb flanked by the markers DXS304 and DXS497. We describe here cosmid contigs covering a region of 900 kb, including the entire MTM1 candidate region. Cosmids from the region were used to construct an enriched cDNA library from this area. Filter grids carrying this library were then screened by hybridization with whole cosmid clones, with CpG island-containing fragments from linking clones located in the area, and with total exon trap products of cosmid clones from the candidate region. In this analysis, 10 new transcripts were identified and localized precisely within the map. Genes in this area are candidates for MTM1 and a number of other diseases localized by genetic linkage studies to the chromosomal band Xq28.

Adult↗
PubMed1996

Assembly of a 1-Mb restriction-mapped cosmid contig spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1.

We describe the assembly of a 1-Mb cosmid contig and restriction map spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1. The map was constructed from 16 smaller contigs assembled by fingerprinting, a BAC and a PAC clone, and 42 previously unmapped cosmids. In most cases, single-step cosmid walks were sufficient to join two previously assembled contigs, and all but one gap was filled from this cosmid contig library. The remaining gap of about 19 kb was spanned with a single BAC and a single PAC clone. EcoRI mapping of a dense set of overlapping clones validated the assembly of the map and indicated a length of 1040 kb for the contig. This high-resolution clone map provides an ideal resource for gene identification through cDNA selection, exon trapping, and DNA sequencing.

Chromosome Mapping↗
PubMed1996

A YAC, P1, and cosmid contig and 17 new polymorphic markers for the Werner syndrome region at 8p12-p21.

A yeast artificial chromosome (YAC), P1, and cosmid clone contig was constructed for the Werner syndrome (WRN) region of chromosome 8p12-p21 and used to clone a candidate gene for WRN. This region also possibly contains a familial breast cancer locus. The contig was initiated by isolating YACs for the glutathione reductase (GSR) gene and extended in either direction by walking techniques. Sequence-tagged site (STS) markers were generated from subclones of 2 GSR YACs and used to identify P1 and cosmid clones. Additional STSs were generated from P1 and cosmid clones and from potential expressed sequences identified by cDNA selection and exon amplification methods. The final contig was assembled by typing 17 YACs, 20 P1 clones, and 109 cosmids for 54 STS markers. The WRN region could be spanned by 2 nonchimeric YACs covering approximately 1.4 Mb. A P1/cosmid contig was established covering the core 700-800 kb of the WRN region. Fifteen new short tandem repeat polymorphisms and 2 biallelic polymorphic markers were identified and included as STSs in the contig. Analysis of these markers in Werner syndrome subjects demonstrates that the candidate WRN gene is in a region of linkage disequilibrium.

Base Sequence↗
PubMed1997

Construction and screening of a cosmid library generated from a somatic cell hybrid bearing human chromosome 15.

A cosmid library has been constructed with DNA isolated from a mouse/human hybrid cell line designated A15, which was previously characterized and shown to retain chromosome 15 as the only human material. The library was generated and stored as 34 independent pools of primary colonies at 8-10,000 colonies per pool. Screening colonies representing pools of this library by hybridization with a human-specific repetitive probe has facilitated the identification of random clones bearing human inserts. To data, 43 unique clones have been isolated and the inserts mapped by fluorescence in situ hybridization (FISH) to chromosome 15. An STS was generated for each of these clones by end sequencing of the inserts. Two of these clones, c36 and MR23, were mapped by FISH to 15q26.1, and end-sequence data revealed homology to different regions of the FES protooncogene. Sequence generated from the other end of the c36 insert was found to match the previously identified and unmapped coding sequence EST00075. In addition to the identification of such random clones, establishment of the library as pools was expected to facilitate the PCR-based identification of unique clones representing specific regions of chromosome 15. Screening of the library pools with primers specific to the FES region led to the recovery of five independent clones facilitating the development of a cosmid contig encompassing the FES gene. One of the cosmids isolated by PCR-based analysis was derived from the same pool as M23 and was subsequently shown to be identical to M23. The data offer the first report of a chromosome 15 cosmid library and demonstrate the value of utilizing pools to evaluate libraries generated from complex sources like somatic cell hybrids.

Animals↗
PubMed1991

Relative order determination of four Yp cosmids on metaphase and interphase chromosomes by two-color competitive in situ hybridization.

Two-color competitive in situ hybridization was used to cytogenetically order four Yp cosmid probes, located in the pseudo-autosomal and TDF regions. The probes were hybridized by pairs to metaphase and interphase chromosomes. On metaphase chromosomes, determination of order between sequences separated by 3 Mb from each other was possible on a statistical basis, whereas the relative position of sequences 0.6 Mb apart could not be determined. On interphase chromosomes the complete order between sequences separated by 0.6-6 Mb was obtained rapidly by measuring the distances between two cosmid spots of every cosmid pair used in 28 to 60 nuclei. Results demonstrate the potential power of fluorescent in situ hybridization at interphase for high resolution cosmid mapping.

Binding, Competitive↗
PubMed1986

A highly polymorphic locus on chromosome 16q revealed by a probe from a chromosome-specific cosmid library.

A cosmid library was constructed from genomic DNA of a human-mouse somatic cell hybrid containing an 11q-16q translocation chromosome as the only human DNA. Cosmids with human inserts were prehybridized with total human DNA and were screened to find probes that revealed highly polymorphic loci. From one such cosmid, CF33-79, a single-copy subclone was isolated which revealed an insertion/deletion polymorphism with at least 11 alleles and a PIC of 0.77. Using a somatic cell hybrid mapping panel, the subclone was mapped to chromosome 16. By in situ hybridization with the entire cosmid used as a probe, chromosomal localization was shown at 16q22----24.

Animals↗
PubMed1987

Use of whole cosmid cloned genomic sequences for chromosomal localization by non-radioactive in situ hybridization.

We report a general procedure which allows the application of whole cosmid cloned genomic sequences for non-radioactive in situ hybridization. The presence of highly repetitive sequences, like Alu and Kpn fragments, is eliminated through competition hybridization with Cot-1 DNA. The method has been tested and optimized with several randomly chosen cosmids of the human thyroglobulin (Tg) gene (8q24). At present, the procedure can be performed with three of the four tested individual cosmids. In cases where a single clone does not result in a specific signal, a larger fragment may be required, which can be accomplished by using two (partially overlapping) cosmids of the same region. The advantages and further potentialities of such a hybridization approach are discussed.

Chromosome Mapping↗
PubMed1986

In vivo cloning of DNA into multicopy cosmids by mini-Mu-cosduction.

A general in vivo procedure for cloning Escherichia coli genes into cosmids has been developed. The method we describe here uses a deleted Mu phage (a mini-Mu) to transpose E. coli genes into cosmids during mini-Mu replication. The resulting cosmids clones are packaged in vivo into lambda phage particles. Plasmids carrying a particular DNA sequence can be selectively recovered after infection of a new host with the in vivo constructed genomic cosmid library. This system was used successfully to clone several E. coli genes.

Bacteriophage lambda↗
PubMed1992

Construction and characterization of radiation hybrids for chromosome 9, and their use in mapping cosmid probes on the chromosome.

Radiation hybrids were produced from a monochromosomal microcell hybrid (PK87-9) which contains only human chromosome 9 with an inserted marker on 9p. Doses of radiation ranging from 1000 to 8000 rads were used to produce a series of hybrids with different size fragments of human chromosome 9. The inserted dominant selectable marker was used to select for hybrids that preferentially maintain fragments of 9p. A panel of 53 radiation hybrids were characterized for 17 chromosome 9 markers. In addition, 17 hybrids were analyzed by fluorescent in situ hybridization (FISH). Hybrids were produced with breaks on both 9p and 9q, many of which appear to contain a single fragment of human chromosome 9. These hybrid cell lines were used to regionally localize 31 cosmids isolated from a chromosome 9 cosmid library. Six cosmids were mapped to intervals on 9p, six cosmids mapped to the centromeric region of the chromosome, and 19 mapped to 9q.

Animals↗
PubMed1993

Cosmid clones from microdissected human chromosomal region 15q11-q13.

A human chromosomal region, 15q11-q13, was microdissected, its DNA was amplified with the primer-linker PCR method, and the PCR products were cloned into a plasmid vector to construct a microclone library. Of 193 microclones analyzed with Southern blot hybridization on hybrid cell panels, 26 (13.5%) were either single-copy (unique) or low-repetitive fragments. By screening of a cosmid library of human genomic DNA using the 26 microclones as probes, 47 positive cosmids were obtained and underwent regional mapping with chromosome fluorescence in situ hybridization (FISH). Sixteen cosmids gave FISH signals at 15p-cen, 5 at 15q11-q13, 6 at 15q22-q26, 3 at other chromosomes, and 17 no signal. These 27 cosmids mapped to chromosome 15 are useful additions to the inventory of DNA markers of this chromosome including the much interested Prader-Willi/Angelman syndrome region.

Base Sequence↗
PubMed1994

Refined mapping of eight cosmid markers on human chromosome 22.

Eight cosmid clones were regionally assigned to small subregions of chromosome 22 by hybridization with a total of 22 somatic cell hybrids. One cosmid was localized to the proximal part of 22q which contained the region commonly deleted in the DiGeorge syndrome. Seven cosmids showing restriction fragment length polymorphisms were localized to the telomeric region distal to the MB locus, which was reported to be frequently deleted in sporadic meningioma. These cosmids, when finely mapped and ordered, are considered useful for the identification of genetic alterations on this chromosome arm.

Chromosome Mapping↗
PubMed1994

Isolation of two contigs of overlapping cosmids derived from human chromosomal band 3p21.1 and identification of 5 new 3p21.1 genes.

Consistent loss of DNA sequences from several regions on the short arm of human chromosome 3 has suggested that multiple tumor suppressor genes reside on chromosome 3p in various types of cancer cells. We have focused our efforts on an analysis of chromosomal band 3p21.1 since aminoacylase-1 (ACY1), which is localized to this band, has been shown to have lower levels of expression in several small cell and non-small cell lung cancer cell lines. Starting with two cosmids within 3p21.1, D3S92 and D3S93, we have isolated two separate contigs of overlapping cosmids within 3p21.1, by screening a library of 5700 chromosome 3-specific cosmid clones. Detailed restriction maps for these two contigs show that they contain multiple clusters of rare cutting restriction endonuclease sites. One contig extends for 100 kb and encompassed both ACY1 and D3S92, and the other extends about 80 kb around the D3S93 locus. Many different restriction fragments derived from these two contigs were found to be evolutionarily conserved and hybridized to distinct message transcripts. These fragments were used to identify homologous cDNAs from an adenogastric cDNA library, and several of these cDNAs were partially sequenced. We have identified five new genes from these two contigs and there is evidence to suggest that several additional genes reside within these cosmid contigs. The genes identified from 3p21.1 were then hybridized to DNA, isolated from a series of lung cancer cell lines and matched normal and tumor DNA from lung cancer patients. No alterations were detected with any of these probes, both at the DNA or RNA levels. A similar analysis with DNA fragments derived from these two genomic regions also failed to detect any alterations.

Animals↗
PubMed1996

Comparative FISH mapping of bovine cosmids to reindeer chromosomes demonstrates conservation of the X-chromosome.

Three X chromosome-specific bovine cosmids were used for fluorescence in situ hybridization mapping on reindeer (Rangifer tarandus) chromosomes, to test whether such large genomic clones could be used for comparative mapping across distantly related species. All three cosmids showed distinct unique hybridization sites on the reindeer X. Comparative map locations of these cosmids, together with the relative C-banding and genome size data on the X chromosomes of the two species, provide preliminary indications that the short and long arms of bovine X correspond, respectively, to the long and short arms of the reindeer X. The study also demonstrates that cosmid clones can be used successfully for comparative mapping across species that diverged 35 million years ago.

Animals↗
PubMed1996

Molecular dissection of a cosmid from a gene-rich region in 17q21 and characterization of a candidate gene for alpha-N-acetylglucosaminidase with two cDNA isoforms.

A cosmid mapped to human Chromosome (Chr) 17q21, c140c10, was found to contain a CpG island. We completed the sequence analysis of c140c10 because of two considerations: the cosmid contained an STS from the 17-beta-hydroxysteroid dehydrogenase gene (17-HSD), which was believed to be a neighbor of the breast cancer susceptibility gene, BRCA1; CpG islands are usually associated downstream and/or upstream of human genes. Computer-based exon trapping of the cosmid sequence revealed putative additional exons. With two of those exons used as a probe to screen human placental cDNA libraries, two cDNA isoforms for a novel gene, designated as ufHSD, were isolated. The amino acid sequence of the open reading frames of the cDNA showed no significant homology to any protein in the data base. However, it is possible that our cDNAs are from the gene for alpha-acetylglucosaminidase, which has recently been localized to the same region. Northern analyses show that the major isoform is expressed in all tissues tested, with the highest expression in blood leukocytes and lowest in brain. Finally, our study has shown that the 46.7-kb cosmid c140c10 encompasses loci for five genes and pseudo-genes: PsiPTP4A, ufHSD, 17-HSDI, 17-HSDII, and 22A1.

Acetylglucosaminidase↗
PubMed1991

Strategy and methods for directly sequencing cosmid clones.

The primer-directed enzymatic sequencing method for sequencing double-stranded DNA templates has made possible the development of new strategies for directly sequencing large DNA molecules. Toward this goal, we have developed a strategy and the necessary techniques to obtain the complete sequence of cosmid clones (double-stranded DNA molecules in the size range of 50 kb). Our present strategy uses the chemical sequencing method to obtain sequence initiation points internal to a cosmid insert and the primer-directed enzymatic DNA sequencing method to extend these sequence contigs. As part of this development we added a nucleotide "chase" solution to the standard T7 sequencing protocol and included the use of both [alpha-32P]-dATP and -dCTP for labeling. With these modifications our double-stranded cosmid DNA sequencing reactions routinely extend well beyond 1000 bp, and film exposure times are kept to a minimum (24 to 48 h). We can routinely separate sequenced DNA fragments, using a 1-m gel system, which can be accurately read (with less than 0.5% error) to distances of 800 bp or more, from the oligomer primer. The strategy and procedures presented here allow the complete sequence of a cosmid clone to be obtained without subcloning.

Base Sequence↗