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At least 1,279 records · Page 71Linked to original sources
PubMed1996

Construction of a YAC contig and an STS map spanning 3.6 megabase pairs in Xp22.1.

We have constructed a 3.6 Mb sequence tagged sites (STS)-based yeast artificial chromosome (YAC) contig, consisting of 58 individual YAC clones, spanning the region PDHA1 and DXS451 on Xp22.1. In addition to establishing the order of PDHA1, ISPK-1, DXS2504, DXS1528 and the 13 known polymorphic loci as Xpter-PDHA1-DXS443-DXS3424-ISPK-1-DXS12 29-DXS2504-DXS1528-DXS365-DXS7101- DXS1683-DXS1052-DXS274-DXS92-DXS1226-DX S41-DXS989-DXS451-Xcen, we have also developed 35 novel STSs from YAC end clones. These results provide a high density of STS markers (approximately 1 per 70 kb). Furthermore, a detailed long-range restriction map of the contig has been constructed with rare-cutter enzymes and this has refined and verified the physical distances between markers inferred from YAC sizes and their STS content. The integration of the physical mapping data with previous genetic mapping data and the use of STSs and non-chimeric YAC clones reported here should facilitate the construction of a transcript map of this region and the positional cloning of disease genes in this portion of Xp22.1.

Base Composition↗
PubMed1996

Integrated physical, genetic, and genic map covering 3 Mb around the human NGF gene (NGFB) at 1p13.

We have characterized 11 overlapping yeast artificial chromosomes (YACs) in the 1p13 region, 8 of them containing the human nerve growth factor (NGF) gene (HGMW-approved symbol NGFB). Sequence-tagged sites (STSs) corresponding to YAC extremities have been designed and used for chromosome assignment on a panel of monochromosomic somatic cell hybrids to check for YAC chimerism, in parallel with analyses by fluorescence in situ hybridization. Determination of end STS content and restriction mapping of the YACs led to the construction of a 3-Mb YAC contig. Four microsatellite markers from the Généthon collection and seven genes known to map to the 1p13 region have been ordered on the contig around the NGF gene. A new gene transcript from the Genexpress catalog has been localized on the contig. This work provides an integrated physical, genetic, and genic map of this chromosome 1 region. It constitutes a basis for determining the structure of the NGF gene and for further characterizing its genic environment.

Animals↗
PubMed1990

Characterization and physical mapping of plasmids of black-pigmented Bacteroides.

Eight species of black-pigmented Bacteroides (BPB) were examined for plasmid content. Three classes of plasmids with molecular sizes of 16.0 kilobase (kb), 5.4 kb and 5.0 kb were found in 7 of 125 Bacteroides intermedius strains. One strain each of Porphyromonas (former Bacteroides) asaccharolyticus and of Bacteroides levii were also shown to have plasmids. However, no plasmids were detected in 90 strains of Porphyromonas (Bacteroides) gingivalis. The plasmids were purified and digested with restriction endonucleases for restriction mapping. The maps obtained in this study have given us information on the scheme of constructing recombinants which may be usable as shuttle vectors, by the recombination of BPB and Escherichia coli plasmids.

Bacteroides↗
PubMed1995

Construction of a 3.7-Mb physical map within human chromosome 20p12 ordering 18 markers in the Alagille syndrome locus.

Alagille syndrome (AGS, MIM 118450) is associated with human chromosome band 20p12. To study this region, we constructed a 3.7-Mb physical map using 36 YACs isolated from the CEPH YAC library with three sequence-tagged sites (STS): D20S503, D20S41, and D20S188. New STSs were obtained from 6 isolated YAC end-fragments. Eighteen markers were ordered on the contig as follows:20ptel-D20S177-D20S175-D20S509- D20S5/D20S503-D20S506-D20S162-D20S504- D20S505-D20S507-D20S188-(D20S6-D20S27- D20S189)-D20S186-D20S41-D20S61-D20S492- D20S508-20pcen. A restriction map with the enzymes AscI, MluI, NotI, SacII, and SfiI was generated, revealing seven putative CpG islands. We established a YAC contig that spans the AGS region and thus will be valuable for cloning candidate genes and searching for DNA polymorphisms segregating with this syndrome.

Alagille Syndrome↗
PubMed1994

The human vigilin gene: identification, chromosomal localization and expression pattern.

Chick vigilin cRNA clones were used to isolate the cognate human gene, by screening a pWE15 genomic library. Three independent cosmid clones were isolated and characterized by restriction mapping. The gene was identified by sequencing an internal EcoRI fragment containing two exons homologous to exon 24 and 25 of the chicken vigilin gene and corresponding to nucleotides 1973-2104 of the human HBP-cDNA. The homology between the chicken and human sequences was 77% and 82% at the cDNA level, and 91% and 100% at the amino acid level. In addition, the analyzed intron/exon boundaries were invariantly conserved. The 5' and 3' regions of the human gene were mapped by Southern analysis of the respective clones with synthetic oligonucleotides. The entire vigilin gene spans a region of about 50 kb and has been assigned to chromosome 2q36-q37.2 (FL-pter value of 0.96 +/- 0.03) by fluorescence in situ hybridization to metaphase spreads from normal peripheral blood lymphocytes. The vigilin gene is localized in a chromosomal region comprising a cluster of collagen genes (COLIVA3, COLVIA3) and the locus of the Waardenburg syndrome I. Only one mRNA species of 4.4 kb is transcribed from the human vigilin gene. In accordance with previous observations on chicken mRNA, the expression of the human vigilin mRNA depends on the stage of cytodifferentiation both in vitro and in situ.

Blotting, Northern↗
PubMed2000

Structural organization and chromosomal localization of the human type II deiodinase gene.

OBJECTIVE: The selenoenzyme type 2 iodothyronine 5' deiodinase (DII) catalyzes the conversion of thyroxine into its active form tri-iodothyronine (T3), modulating thyroid hormone homeostasis in a local, tissue-specific manner. The amphibian, rodent and human cDNAs encoding this enzyme have been recently cloned and expressed. At present, little information regarding the genomic structure of mammalian DII is available. DESIGN AND METHODS: The complete structure, including intron-exon junctions, of the human DII (hDII) gene was obtained by long PCR and rapid amplification of cDNA ends (RACE). Chromosomal assignment of the hDII gene was performed by fluorescence in situ hybridization using a highly specific probe. RESULTS AND CONCLUSIONS: Our data demonstrated that hDII is a single copy gene located on chromosome 14, position 14q24.3. The gene spans over 15 kb, and the 7 kb transcript is encoded by three exons of 149 bp, 273 bp and 6.6 kb separated respectively by two 274 bp and 7.4 kb introns. A restriction map of the hDII gene is also reported. These data will help in further studies of the role of DII in the maintenance of peripheral thyroid hormone homeostasis.

Alternative Splicing↗
PubMed1993

Analysis of rearranged immunoglobulin genes indicating a process of clonal evolution in chronic lymphocytic leukaemia.

Chronic lymphocytic leukaemia (CLL) is known to be a stable monoclonal neoplasm. In contrast to early studies demonstrating no more than two hybridizing immunoglobulin heavy chain bands corresponding to the two expected alleles, we have demonstrated an unexpected multiband pattern when the HindIII-digested DNA samples from 38 CLL patients were analysed by Southern blot hybridization using JH and C mu gene probes. In order to characterize the genetic basis for the multiband pattern, we molecularly cloned the immunoglobulin heavy chain genes of one of the patients whose leukaemic DNA sample demonstrated three hybridizing JH bands and a loss of the germline band. The cloned rearranged immunoglobulin genes could be divided, based on the restriction mapping and the hybridization with the various probes, into two basic patterns representing two alleles. In one of the cloned rearranged immunoglobulin genes a secondary rearrangement occurred that resulted in the addition of 300 base-pair long sequence into the switch region, and the creation of a HindIII restriction site. The results of the study suggest that clonal evolution occurs in some CLL, and that many of these neoplasms are indeed oligoclonal due to the accumulation of secondary genetic changes.

Antibodies, Neoplasm↗
PubMed1999

The human platelet alphaIIb gene is not closely linked to its integrin partner beta3.

alphaIIbb3 integrin is a heterodimeric receptor facilitating platelet aggregation. Both genes are on chromosome 17q21.32. Intergenic distance between them has been reported to be 125 to 260 kilobasepairs (kb) by pulsed-field gel electrophoresis (PFGE) genomic analysis, suggesting that they may be regulated coordinately during megakaryopoiesis. In contrast, other studies suggest these genes are greater than 2.0 megabasepairs (mb) apart. Because of the potential biological implications of having these two megakaryocytic-specific genes contiguous, we attempted to resolve this discrepancy. Taking advantage of large kindreds with mutations in either alphaIIb or beta3, we have developed a genetic linkage map between the thyroid receptor hormone-1 gene (THRA1) and beta3 as follows: cen-THRA1-BRCA1-D17S579/alphaIIb-beta3-qte r, with a distance of 1.3 centiMorgans (cM) between alphaIIb and beta3 and the two genes being oriented in the same direction. PFGE genomic and YAC clone analysis showed that the beta3 gene is distal and >/=365 kb upstream of alphaIIb. Additional restriction mapping shows alphaIIb is linked to the erythrocyte band 3 (EPB3) gene, and beta3 to the homeobox HOX2b gene. Analysis of alphaIIb(+)-BAC and P1 clones confirm that the EPB3 gene is approximately 110 kb downstream of the alphaIIb gene. Sequencing the region surrounding the human alphaIIb locus showed the Granulin gene approximately 18 kb downstream to alphaIIb, and the KIAA0553 gene approximately 5.7 kb upstream. This organization is conserved in the murine sequence. These studies show that alphaIIb and beta3 are not closely linked, with alphaIIb flanked by nonmegakaryocytic genes, and imply that they are unlikely to share common regulatory domains during megakaryopoiesis.

Anion Exchange Protein 1, Erythrocyte↗
PubMed1992

Walking, cloning, and mapping with yeast artificial chromosomes: a contig encompassing D21S13 and D21S16.

Chromosome 21 has often been used as a model system for the development of genome mapping and cloning strategies in humans. In this report methods for systematic chromosome walking, cloning, and mapping are exemplified in the construction of a 1.5-Mb yeast artificial chromosome (YAC) contig encompassing and extending 400 kb beyond each of the genetic loci D21S13 and D21S16. Isolation of insert-terminal sequences from YACs in this contig provides a set of closely spaced physical markers. These have been used to generate a long-range genomic restriction map.

Base Sequence↗
PubMed1997

Closely spaced tandem arrangement of AQP2, AQP5, and AQP6 genes in a 27-kilobase segment at chromosome locus 12q13.

The aquaporins (AQPs) are a family of water-transporting proteins that facilitate osmotically driven water movement across cell plasma membranes. Among the seven human aquaporins cloned to date (AQPs 0-6), genes encoding the four most closely related aquaporins (AQP0, AQP2, AQP5, and AQP6) have been mapped to chromosome band 12q13, suggesting an aquaporin family gene cluster at this locus. To construct a physical map and identify novel aquaporin gene members on this cluster, a human CEPH B yeast artificial chromosome (YAC) library was screened by PCR using primers derived from exon 4 of AQP2 and AQP0 genes. A YAC clone with 200 kb of human DNA was isolated and analyzed. Primary pulsed-field gel electrophoresis and Southern blot analysis indicated the presence of AQP2, AQP5, and AQP6 genes, but not AQP0. Restriction mapping and PCR analysis yielded a precise physical map in which the three aquaporin genes span only approximately 27 kb in the order, transcriptional orientation, and spacer length 5'-AQP2-5 kb spacer-AQP5-7 kb spacer-AQP6-3'.

Aquaporin 5↗
PubMed1993

The human C/EBP delta (CRP3/CELF) gene: structure and chromosomal localization.

In an attempt to identify C/EBP-like transcription factors expressed in the prostate, a cDNA homologous to the mouse C/EBP delta (CRP3) and the rat CELF gene was isolated. A genomic clone containing the entire C/EBP delta gene was isolated using a cDNA fragment as a probe. The gene was characterized by restriction mapping and sequence analysis. By fluorescence in situ hybridization, using the biotinylated genomic clone as a probe, the C/EBP delta gene was assigned to the pericentromeric region of human chromosome 8, most probably to 8q11. This chromosomal localization was confirmed by analysis of a panel of human x hamster somatic cell hybrid DNA samples with a C/EBP delta-specific STS. As a result, the C/EBP delta gene could be positioned between the PLAT and the MOS loci.

Amino Acid Sequence↗
PubMed1997

The resistance and integrase genes of pACM1, a conjugative multiple-resistance plasmid, from Klebsiella oxytoca.

pACM1 is an 85-kb conjugative plasmid from a clinical isolate of Klebsiella oxytoca that encodes resistance to beta-lactams (mediated by SHV-5 extended spectrum beta-lactamase), trimethoprim, sulfonamides, tetracycline, aminoglycosides, and mercuric chloride. The expression of the aminoglycoside resistance is difficult to detect, which could have clinical implications. A region of pACM1 containing five resistance genes and two putative integrons was characterized by restriction mapping and partial DNA sequencing. One integron appears to be class I (sull type); the second lacks a recognizable 3' conserved segment. Neither integron has the BamHI site predicted for the 5' conserved segment. Plasmids encoding SHV-5 from other bacterial strains appear to be closely related to pACM1 by restriction enzyme analysis, but have resistance/ integron regions that vary in size and content from that of pACM1. Integrase-mediated recombination might be responsible for genetic divergence in a widely distributed family of pACM1-like plasmids.

Amino Acid Sequence↗
PubMed1990

Linear plasmid DNAs of the plant pathogenic fungus Rhizoctonia solani with unique terminal structures.

Three linear DNA plasmids were found in isolate RI-64 of anastomosis group 4 (AG-4) of Rhizoctonia solani. These plasmids, designated pRS64-1, -2, and -3, possessed the same size of 2.7 kb. Restriction mapping and Southern hybridization analysis of pRS64-1, -2, and -3 revealed the presence of homologous regions at both termini. The plasmid DNAs were resistant to both 3'-exonuclease and 5'-exonuclease even after treatment with proteinase K or alkali. The length of both terminal fragments that were generated by restriction endonuclease digestion was doubled under the denaturation condition, indicating that the linear plasmid DNAs have hairpin loops at both termini. Southern blotting analysis of total DNA showed the presence of two types of dimeric forms of pRS64 DNA. One is a head-to-head dimer and the other is a tail-to-tail dimer. The role of these unique DNA structures in replication of the plasmids is discussed.

Base Sequence↗
PubMed1991

Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA.

Restriction maps were constructed of enzymically amplified 16S rRNA genes (rDNA) isolated from eight Clostridium species. Using maximum parsimony, a dendrogram was constructed from these and published 16S rRNA sequence data. Two distinct clusters were identified: cluster I contained C. difficile, C. sordelli, and C. bifermentans, and showed 30 of 35 restriction sites in common; cluster II contained C. tetani, C. perfringens C. sporogenes and C. botulinum C and G, and showed 20 of 35 restriction sites in common. Further analysis of cluster I organisms revealed that of five HpaII fragments, two were found in equal amounts in all organisms, one was found in varying amounts in all organisms, and two were found, in varying amounts, only in C. sordelli and C. bifermentans. C. sordelli-specific and C. bifermentans-specific HpaII fragments were demonstrated by Southern hybridization of rDNA. One HpaII site within the rDNA was present on most alleles in C. bifermentans, present on a minority of alleles in C. sordelli and absent in C. difficile. This suggested that there were two 16S rRNA alleles with different sequences present within each of the genomes of C. bifermentans and C. sordelli.

Alleles↗
PubMed1989

Structural differences in the renin gene of Dahl salt-sensitive and salt-resistant rats.

Genomic libraries in lambda EMBL4 phage were constructed from both inbred Dahl salt-hypertension-sensitive (S) and inbred Dahl salt-hypertension-resistant (R) rats. Overlapping clones containing the renin genes were isolated from these libraries by screening with a renin cDNA probe. Clones were characterized by a combination of restriction mapping and Southern blot analysis. The results showed that the S-rat renin gene is remarkably different from the R-rat renin gene. The major differences are 1) a 1.2-kilobase (kb) insertion in the first intron of the S-gene which accounts for most of the restriction fragment length polymorphisms found in the renin genes between S and R strains, such as those generated with Bg/II [2.7 kb (S)/1.5 kb (R)], EcoRI [6.4 kb (S)/5.2 kb (R)], and HindIII [9.6 kb (S)/8.4 kb (R)]; 2) an additional HindIII site located at the 3' end of the R-gene which accounts for another HindIII restriction fragment length polymorphisms [25 kb (S)/22 kb, 3.4 kb (R)]; 3) two SmaI sites at the 5' flanking region of the first exon of the S-gene, whereas there is only one SmaI site in the corresponding region of the R-gene; and 4) three AvaI sites in the first intron of the S-gene in contrast to two AvaI sites in the same region of the R-gene These differences in the renin genes of Dahl rats might affect renin gene expression, which could account for the known strain differences in plasma and tissue renin activities. These structural studies provide a basis for genetic investigation into the relationship of the renin gene to blood pressure in Dahl rats.

Animals↗
PubMed1989

Human retinoblastoma gene: long-range mapping and analysis of its deletion in a breast cancer cell line.

Mutational inactivation of the retinoblastoma (RB) gene is considered a fundamental event in the formation of several types of human cancer. A substantial proportion of RB gene mutations are partial or complete deletions that extend an unknown distance beyond one or both ends of the gene. To provide a framework for measuring the extent of these deletions, we have constructed a long-range restriction map of SfiI sites spanning 850 kilobases around the RB gene. This map was applied in a molecular analysis of RB gene deletion in breast cancer cell line MB468. A previous study of this cell line demonstrated deletion of the entire RB gene except for exons 1 and 2 (E. Y.-H. P. Lee, H. To, J.-Y. Shew, R. Bookstein, P. Scully, and W.-H. Lee, Science 241:218-221, 1988). Genomic clones containing the deletion junction were isolated from a library made from MB468 DNA. A probe obtained from the far side of the deletion junction was used to localize and clone the unknown 3' endpoint, demonstrating that the chromosomal mutation in this case was a simple deletion spanning 200 kilobases. Sequence analysis of the deletion junction indicated a conservative deletion with no loss or gain of nucleotides. The deletion endpoints had no sequence homology to each other or to any repetitive sequence family, such as Alu, so the recombination event was illegitimate. Structural analysis of this and other RB gene deletions is important for understanding molecular mechanisms of recessive oncogenesis.

Base Sequence↗
PubMed1989

Mitochondrial DNA polymorphism in native Philippine cattle based on restriction endonuclease cleavage patterns.

An analysis of patterns of cleavage of mtDNA by restriction endonucleases was performed for nine individuals from the Philippine population of native cattle. MtDNA polymorphisms were detected in the restriction patterns generated by the following six enzymes, BamHI, BglII, EcoRV, HindIII, PstI, and ScaI. The restriction patterns showing polymorphisms were distributed nonrandomly among the nine individuals examined from the Philippine population of native cattle, indicating the existence of two separate types of mtDNA. These two types of mtDNA are very different from each other, at the level of subspecies. Since the native Philippine cattle are considered to represent an admixture of European and Indian cattle, the two types of mtDNA must be derived from the mtDNAs of both varieties. The polymorphic sites in mtDNA have been located on a restriction map, and the nucleotide substitutions at some of the sites have also been estimated.

Animals↗
PubMed1989

Characterization of the plasmids of Moraxella bovis.

Restriction endonuclease digestions were performed on plasmids purified from Moraxella bovis isolates GRS, Newport, and IBH64. It was determined from single and double digestions of plasmid DNA that GRS and Newport isolates carried 3 large plasmids having molecular sizes of 43.8, 41.3, and 32.8 kilobases (kb). Digestion of the 3 large plasmids and restriction endonucleases Hae III, HindIII, Nde I, and Ava I strongly indicated that these isolates shared structurally identical large plasmids. Timed single digestions with Ava I revealed that the IBH64 isolate carried 2 large plasmids having molecular sizes of 45 and 32.8 kb. The 32.8-kb plasmid was the only large plasmid that appeared to be shared by all 3 M bovis isolates. Two isolates, Newport and IBH64, carried small plasmids in addition to the large plasmids. Restriction maps were constructed for the 43.8-, 41.3-, and 32.8-kb plasmids.

Animals↗