SEARCH · Search PubMed

Results for “Restriction Mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources

PubMed1993

Characterization of human T-lymphotropic virus type I- and II-infected T-cell lines: antigenic, phenotypic, and genotypic analysis.

Eighteen long-term T-cell lines were established from peripheral blood mononuclear cells of individuals infected with human T-lymphotropic virus type I (HTLV-I) or II (HTLV-II). These cell lines (10 HTLV-I and 8 HTLV-II), representing diverse pathologic profiles and geographic regions, have been in culture for over 6 months and have constitutively produced p24gag antigen. Antigenic characterization of the cell lines by Western blot analysis demonstrated that all but one produced gag (p24) and env (gp46 or gp52) structural proteins; one HTLV-I-infected cell line exhibited an aberrant protein profile. Phenotypic analysis of the HTLV-infected cell lines demonstrated phenotypes consistent with activated T-cells (CD5+, CD25+, HLA-DR+). The HTLV-I-infected cell lines were predominantly CD4+ (IR, FS, A212, SP, 1657, 1742, 3669, 1996, and 3614), whereas EG was CD8+. The HTLV-II-infected cell lines were either CD4+ (H2A, Y17, G12.1), CD8+ (H1H, H2E, Y03, Y06), or both (H1B). Restriction map analysis and subtyping of the viral genomes demonstrated heterogeneity among these isolates. Of the HTLV-I-infected cell lines, six were subtype II, one was subtype III and, on the basis of additional restriction sites, another subtype, tentatively classified as subtype IV, could be identified for three of the HTLV-I-infected cell lines. Of the HTLV-II-infected cell lines, six were subtype HTLV-IIa and two were subtype HTLV-IIb. While the majority of the cell lines resemble the prototypic HTLV-I-infected (MT-2) and HTLV-II-infected (MoT) cell lines, the antigenic, phenotypic, and genotypic data collectively demonstrate heterogeneity among viral isolates representing diverse geographic regions.

Adult↗

PubMed1989

Physical localization of two DNA markers closely linked to the cystic fibrosis locus by pulsed-field gel electrophoresis.

Our previous linkage analysis suggested that the DNA segment D7S122 is located between MET and D7S8, the two genetic markers that are thought to flank the cystic fibrosis locus (CF). Subsequent chromosome walking experiments revealed that D7S122 in within close distance to another randomly isolated DNA marker, D7S340. To determine the physical relationship among D7S122, D7S340, MET, and D7S8, we have constructed a long-range restriction map of the region containing these four DNA segments, by using DNA from a human/hamster somatic hybrid cell line 4AF-KO15 (containing a single human chromosome 7) and a series of rare-cutting restriction enzymes. The combined results of complete, partial, and double digestion analyses confirm that D7S122 and D7S340 are located between MET and D7S8. The order of these markers is MET-D7S340-D7S122-D7S8, with distance intervals of approximately 500, 10, and 980 kbp, respectively. Together with family analysis, this information will be useful for eventual identification of the CF gene.

Cystic Fibrosis↗

PubMed1987

A new method for the physical and genetic mapping of large plasmids: application to the localisation of the virulence determinants on the 90 kb plasmid of Salmonella typhimurium.

A new method based on transposon-promoted deletions was used to generate a set of deletions in the 90 kb virulence plasmid of Salmonella typhimurium. The analysis of 16 deletion mutants allowed: (1) construction of the restriction map of the plasmid for HindIII, BamHI and BglII; (2) localisation of the plasmid region involved in virulence; (3) identification of two functional replicons on the plasmid.

DNA Mutational Analysis↗

PubMed2001

High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice.

Large-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.

Centromere↗

PubMed1989

Physical mapping of a family of interferon-activated genes, serum amyloid P-component, and alpha-spectrin on mouse chromosome 1.

This report defines genetic and physical relationships among alpha-spectrin (Spna-1), serum amyloid P-component (Sap), and a family of interferon-activated genes, provisionally designated Ifi202, Ifi203, and Ifi204. By linkage analysis using a large panel of interspecific backcross mice, Sap, Ifi202, and Ifi204 were shown to be tightly linked to Spna-1 on distal mouse chromosome 1. By pulsed field electrophoresis, a genomic restriction map of 6400 kb of distal mouse chromosome 1 was generated, linking genes encoding Sap, (Ifi202, Ifi203, Ifi204), and Spna-1 in that order within 450-1000 kb (where the genes within brackets were not ordered). The interferon-activated genes Ifi202, Ifi203, and Ifi204 were linked within 75-150 kb. Furthermore, genes transcriptionally activated by cytokines, namely Sap, Ifi202, Ifi203, and Ifi204, were located within 450 kb. These studies suggest the possibility that selective pressure may maintain in physical proximity gene clusters which are under coordinate transcriptional control.

Animals↗

PubMed1990

Genetic and physical map of the von Recklinghausen neurofibromatosis (NF1) region on chromosome 17.

The von Recklinghausen neurofibromatosis 1 (NF1) locus has been previously assigned to the proximal long arm of chromosome 17, and two NF1 patients have been identified who have constitutional balanced translocations involving 17q11.2. We have constructed a cosmid library from a chromosome-mediated gene transfectant, KLT8, that contains approximately 10% of chromosome 17, including 17q11.2. Cosmids isolated from this library have been mapped across a panel of somatic cell hybrids, including the hybrids from the two patients, and have been localized to seven small regions of proximal 17q. We have 5 cosmids that map directly above the two NF1 translocations, and 11 cosmids that map directly below. Of these, 2 cosmids in each region are linked to the disease locus and 3 of these cosmids show no recombination. One distal cosmid, 2B/B35, detects the two NF1 translocations by pulsed-field gel analysis and has been used to produce a long-range restriction map that covers the translocations.

Blotting, Southern↗

PubMed1995

Analysis of molluscum contagiosum virus genomes isolated in Japan.

The genomes of 477 Japanese strains of molluscum contagiosum virus (MCV) were analyzed using an in-gel digestion method with the restriction enzyme BamHI, and classified into four types, including a newly detected type (MCV type 4). All type 1 (MCV-1) genomes examined so far in Japan showed a common difference from the genome of the MCV-1 prototype (MCV-1p), the type reported to be most prevalent in Europe. The common markers of the variants of MCV-1 were 24-kbp fusion fragments generated by the loss of a BamHI site between the D2 and F fragments of MCV-1p. These variants of MCV-1 were classified into three groups (MCV-1va, MCV-1vb, MCV-1vc), with the variability among them being due to additions and losses of BamHI sites located in the right terminus and around the E and I fragments of MCV-1va. The restriction map of MCV-4 was generated and lined up with those of the other types. Cross-hybridization analysis revealed that the organization of all types of MCV genomes were essentially colinear. Considerable numbers of BamHI restriction sites were conserved between MCV-2 and 4, indicating a close analogy between them. The overall prevalence of MCV, as shown by the ratios of MCV-1 (MCV-1p):MCV-2:MCV-3:MCV-4, was 436(0):13:24:4. Thus, the molecular epidemiology of MCV in Japan is characterized by the absence of the European prototype of MCV-1, the exclusive occurrence and abundance of variants of MCV-1, a greater prevalence of MCV-3 over MCV-2, and the presence of MCV-4.

Genetic Variation↗

PubMed1993

Different modes of hypervariability in (GATA)n simple sequence repeat loci.

Only a few prominent simple sequence repeat (SSR) loci of the type (GATA)n are found in the genome of the mealmoth Ephestia kuehniella Zeller. Therefore this moth was chosen as a model organism for the genetic and molecular analysis of hypervariability of SSR loci. We characterized alleles of (GATA)n loci in different Ephestia strains by cloning and genomic restriction mapping. Some variants appeared to be mere variable number of tandem repeat (VNTR) alleles, others showed considerable changes in the sequence neighbourhood of the GATA repeats. These may be produced by major rearrangements or by transposition of the (GATA)n block together with flanking sequences into a different sequence environment.

Alleles↗

PubMed1981

Organization and expression of multiple actin genes in the sea urchin.

A set of at least 11 actin genes has been isolated from genomic recombinant deoxyribonucleic acid libraries of the sea urchin Strongylocentrotus purpuratus. Most of the isolates derive from a library which represents the genome of a single animal. There are at least five distinct types of sea urchin actin gene, some of which are represented by multiple copies in the genome. The actin gene types are distinguished by nonhomologous flanking sequences and intervening sequences, though the protein coding sequences appear in most cases to be quite similar. Eight of the 11 genes isolated have been recovered in lambda recombinants that contain two actin genes, linked at 5- to 9-kilobase distances. Restriction map overlaps suggest that the genome contains an array of at least three of these genes spaced over about 30 kilobases of deoxyribonucleic acid. In the linkage patterns observed, actin genes of diverse types were linked to each other. In early embryos, actin messenger ribonucleic acid (RNA) transcripts of 1.8 and 2.2 kilobases were found, and the longer of these transcripts was more prevalent in the maternal RNA of the egg. From RNA gel blot experiments, we conclude that the two transcripts derive from different actin gene types. Different repetitive sequences were located to either side of most of the actin genes, and in most observed cases the repeat sequences which were adjacent to actin genes of a given type were similar. The repeat sequences flanking the actin genes belonged to families which were transcribed, but those repeats in the neighborhood of the actin genes which have been investigated were not themselves represented in the stable RNAs of eggs or early embryos.

Actins↗

PubMed1989

Organisation of the mitochondrial genome from Atlantic salmon (Salmo salar).

A restriction map of Atlantic salmon mitochondrial DNA was constructed. The smallest XbaI fragment of the salmon mitochondrial genome was cloned and subjected to partial DNA sequence analysis. This fragment contains the genes for ATPase 6 and cytochrome oxidase III. The putative organisation of the mitochondrial genome relative to the physical map is shown.

Amino Acid Sequence↗

PubMed1992

Physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1403.

A combined physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1403 was determined. We constructed a restriction map for the NotI, ApaI, and SmaI enzymes. The order of the restriction fragments was determined by using the randomly integrative plasmid pRL1 and by performing indirect end-labeling experiments. The strain IL1403 chromosome was found to be circular and 2,420 kb in size. A total of 24 chromosomal markers were mapped on the chromosome by performing hybridization experiments with gene probes for L. lactis and various other bacteria. Integration of pRC1-derived plasmids via homologous recombination allowed more precise location of some lactococcal genes and allowed us to determine the orientation of these genes on the chromosome. Recurrent sequences, such as insertion elements and rRNA gene (rrn) clusters, were also mapped. At least seven copies of IS1076 were present and were located on 50% of the chromosome. In contrast, no copy of ISS1RS was detected. Six ribosomal operons were found on the strain IL1403 chromosome; five were located on 16% of the chromosome and were transcribed in the same direction. A comparison of the physical maps of L. lactis subsp. lactis IL1403 and DL11 showed that these two strains are closely related and that the variable regions are located mainly near the rrn gene clusters. In contrast, despite major restriction pattern dissimilarities between L. lactis IL1403 and MG1363, the overall genetic organization of the genome seems to be conserved between these two strains.

Chromosomes, Bacterial↗

PubMed1990

Analysis of the C4 genes in baleen whales using a human cDNA probe.

We have used a human C4 cDNA probe to investigate the complement component C4 gene in four members of the family Balaenopteridae: fin whale (Balaenoptera physalus), sei whale (B. borealis), minke whale (B. acutorostrata), and bryde's whale (B. edeni). Restriction mapping of genomic DNA from the first three species suggests the presence of only one locus in these species, and also shows that the C4 genes in the three species are very similar. We have used 14 restriction endonucleases to investigate the restriction fragment length polymorphism (RFLP) of fin whales, 13 enzymes for sei whales, and 8 enzymes for the minke whale. No polymorphism was seen in DNA from the five minke whale samples, but Rsa I and Taq I restriction enzymes gave polymorphism in fin and sei whales whereas Hind III and Msp I restriction enzymes showed polymorphism in sei whales only. Only one bryde's whale sample was available for investigation. The study of DNA available from mother-fetus pairs from the two polymorphic species demonstrated a simple, two-allele transmission of RFLP alleles.

Animals↗

PubMed1996

Long-range mapping and construction of a YAC contig within the cat eye syndrome critical region.

Cat eye syndrome (CES) is typically associated with a supernumerary bisatellited marker chromosome derived from human chromosome 22pter to 22q11.2. The region of 22q duplicated in the typical CES marker chromosome extends between the centromere and locus D22S36. We have constructed a long-range restriction map of this region using pulsed-field gel electrophoresis and probes to 10 loci (11 probes). The map covers -3.6 Mb. We have also used 15 loci to construct a yeast artificial chromosome contig, which encompasses about half of the region critical to the production of the CES phenotype (centromere to D22S57). Thus, the CES critical region has been mapped and a substantial portion of it cloned in preparation for the isolation of genes in this region.

Abnormalities, Multiple↗

PubMed1996

Genomic organization of TEL: the human ETS-variant gene 6.

We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap between the two contigs, 2 kb in size, was closed by PCR. The contigs contain the complete coding sequence and the 5' and 3' UTRs of ETV6. Eight exons accounting for the ETV6 cDNA sequence were identified. The helix-loop-helix (HLH) motif is coded by exons 3 and 4, whereas exons 6-8 code for the ETS DNA-binding domain. All introns show consensus 5' donor and 3' acceptor splice sites. Introns 1 and 2 span 100 and 82 kb, respectively, and introns 3-7 range from 15 to 1.3 kb. An alternative exon 1 (exon 1B) is localized in intron 2. The 5' end of the ETV6 gene is associated with a CpG island characterized by the presence of four Notl, four Sacll, and three BssHll recognition sites and several SP1- and AP2-binding motifs. Alternative polyadenylation at the 3' end of the ETV6 gene generates the three transcripts of 6200, 4300, and 2400 nucleotides, respectively. The ETV6 gene spans 240 kb and is flanked at its 5' and 3' end by D12S1697 and D12S98, respectively. The markers D12S1095 and D12S89 are located in the first intron. Two new DNA polymorphisms were identified in the ETV6 gene, which will be useful for the analysis of loss of heterozygosity reported for the ETV6 gene in leukemia.

Base Sequence↗

PubMed1989

Physical fine-mapping of a deletion spanning the Norrie gene.

Norrie disease (ND), atrophia bulborum hereditaria, is caused by a gene defect on the proximal short arm of the X-chromosome. As shown by us and others, microdeletions spanning the DXS7 locus are not uncommon in this disorder, and there is recent evidence that, at least in some of the Norrie deletion patients, the monoamine oxidase (MAO) A and B genes are deleted as well. Molecular hybridization experiments with 19 cloned DNA fragments have enabled us to construct a preliminary long-range restriction map around DXS77, DXS7, MAO-A and MAO-B, and to localize the distal end point of an ND deletion between DXS77 and DXS7.

Blindness↗

PubMed1988

The human T cell receptor alpha-delta locus: a physical map of the variable, joining and constant region genes.

In this study a physical macro-restriction map of the entire human alpha locus that spans about 1000 kilobase pairs and includes the V alpha, J alpha and C alpha genes is presented. Evidence is provided that gene duplications were involved in the increase of genomic diversity of V alpha genes. In addition, we show a detailed map of a 40-kb region located approximately 100 kg upstream of the human C alpha gene. Direct evidence is provided to support that the human alpha chain locus, like the murine, also contains another T cell constant region gene in the alpha chain locus, the human delta chain gene. In addition, two J segments and one D segment have been identified. Using these genomic probes, we show that several T cell lines, including those known to express the surface gamma/delta heterodimer, have rearranged this region. The design of two separate centers of rearrangement within one locus that are involved in rearrangement events at different times, and the presence of high number of J segments in this region, may render the locus highly vulnerable to chromosomal translocation during T cell development.

Cell Line↗

PubMed1989

Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution.

The mitochondrial (mt) DNA from the sea star Pisaster ochraceus has been isolated, restriction-mapped, and cloned into plasmid vectors. Both ribosomal RNA genes, the genes for 12 of the 13 mitochondrial proteins, and 11 of the tRNA genes have been localized by DNA sequence analyses. The sequence arrangement of the genes is markedly different from that seen in sea urchin mitochondrial DNA. A segment of the DNA molecule extending from tRNA(pro), including the tRNA cluster, ND1, ND2, and 16S genes, is inverted in relation to the sea urchin genome. The resulting gene order in the sea star is 12S, 16S, ND2, tRNA cluster, COI. As a result of the inversion, the transcriptional polarity of ND1, ND2, and 16S genes are opposite to that of the 12S and COI genes. The arrangement and transcriptional polarity of the other genes mapped here is the same as seen in urchin.

Animals↗

PubMed1995

Deletion in human chromosome region 12q13-15 by integration of human papillomavirus DNA in a cervical carcinoma cell line.

In human cervical carcinomas papillomavirus DNA is frequently integrated in the cell genome. We have cloned the integration site of human papillomavirus-18 DNA in human chromosome region 12q13-15 present in the SW756 cervical carcinoma cell line. Viral DNA is broken from nucleotides 2643 to 3418 in the E1 and E2 open reading frames, resulting in a deletion of 775 bases of viral DNA. Cloning and sequence analysis of the rearranged and germline alleles shows that there is no homology between the target cellular and viral DNA, suggesting it is a nonhomologous recombination. The target cellular region is called papillomavirus associated locus 2 (PAL2). The 5'- and 3'-flanking probes derived from the hybrid viral-cellular clone detect completely different germline restriction fragments in DNA from cells with normal chromosome 12. There is no overlap between the restriction maps of the target germline clones obtained with 5'- and 3'-flanking probes. Probes from these germline clones beyond the breakpoint position do not detect any DNA rearrangement in SW756 cells DNA. These data prove that there is a deletion of cellular DNA as consequence of the integration, with an estimated minimum size of 14 kilobases. Both cellular flanking probes are outside the amplicon of this chromosome region identified in the OSA and RMS13 sarcoma cell lines, comprising SAS-CHOP-CDK4-MDM2 genes and where translocation breakpoints are located in liposarcomas. The integration at 12q13-15 might have been selected by its contribution to the tumor phenotype.

Alleles↗