Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Contig 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.

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

At least 955 records · Page 53Linked to original sources
PubMed1995

A radiation hybrid map with 60 loci covering the entire short arm of chromosome 12.

We present a high-resolution radiation hybrid map of the short arm of human chromosome 12 containing 60 loci, including 44 STSs within or closely associated with expressed sequences, 11 highly polymorphic markers, 2 anonymous sequences, 2 subtelomeric sequences, and 1 centromeric sequence. The 60 loci fell into 48 unique retention patterns, providing a comprehensive map covering the entire short arm of chromosome 12 with an average resolution of approximately 800 kb. Twenty-two unique positions were ordered in a 1000:1 framework map with an average resolution of 1.8 Mb. The proposed order is in good agreement with recently published genetic maps, high-resolution FISH maps, and YAC contigs. The noted inconsistencies involved neighboring loci permutations. Our observations further suggest the existence of chromosomal "hot spots" for breakage during irradiation. In three regions an usually high number of breaks was noted between neighboring loci compared to the physical distance derived from existing YAC contigs. Some of these hot spots seem to coincide with known chromosomal aberrations, of which at least two have been involved in the etiology of cancer.

Animals↗
PubMed1997

Dynamic molecular combing: stretching the whole human genome for high-resolution studies.

DNA in amounts representative of hundreds of eukaryotic genomes was extended on silanized surfaces by dynamic molecular combing. The precise measurement of hybridized DNA probes was achieved directly without requiring normalization. This approach was validated with the high-resolution mapping of cosmid contigs on a yeast artificial chromosome (YAC) within yeast genomic DNA. It was extended to human genomic DNA for precise measurements ranging from 7 to 150 kilobases, of gaps within a contig, and of microdeletions in the tuberous sclerosis 2 gene on patients' DNA. The simplicity, reproducibility, and precision of this approach makes it a powerful tool for a variety of genomic studies.

Calpain↗
PubMed1994

The P1 vector system for the preparation and screening of genomic libraries.

In retrospect, it is remarkable how swiftly the P1 cloning system has progressed in only a few years from a novel cloning system to one now widely used for the production of recombinant libraries and the building of physical maps. As the libraries become larger, better characterized and more widely distributed, we certainly will see a blossoming of research articles and techniques based on the use of P1 recombinant clones. Specifically, we can look forward to scanning P1 clones for expressed sequences (N. Sternberg, personal communication), routine retrofitting of P1 clones with a combination of transposon and P1 transduction techniques (3), the random or loxP-directed (68,69) insertion of P1 clones into host genomes and the subsequent production of transgenic animals (63), a further use of P1 clones in the building of contigs and physical maps, an a higher in vitro cloning efficiency due to the purification of the P1 pacase proteins used during in vitro packaging (70). In summary, P1 bacteriophage cloning is favorably impacting research today and will continue to fill an important niche as a genomic cloning system.

Animals↗
PubMed1994

Cloning and chromosomal organization of a gene encoding a putative amino-acid permease from Saccharomyces cerevisiae.

A new member of the yeast amino acid (aa) permease gene family has been cloned, mapped and sequenced. The sequence of the PAP1 (putative aa permease 1) gene contains an open reading frame of 566 aa corresponding to a polypeptide with a calculated M(r) of 62,704. Its hydropathy profile suggests the presence of 13 membrane-spanning regions and a charged N-terminal domain. It does not resemble hydrophobic signal sequences found in secreted proteins. Hence, PAP1 encodes a protein with characteristics typical of integral membrane proteins translocating ligands across cellular membranes. Sequence comparisons indicate strong homology to the five known aa permeases of Saccharomyces cerevisiae and to an aa transporter in Trichoderma harzianum. Primer extension analysis revealed one major and one minor transcription start point located 121 and 125 nucleotides upstream from the ATG start codon, corresponding to a 2.1-kb transcript. PAP1 was mapped in a contig of three known (DBF4, TPI and HEM12), but so far unlinked, genes on chromosome IV.

Amino Acid Sequence↗
PubMed1991

Identification of multiple CpG islands and associated conserved sequences in a candidate region for the Huntington disease gene.

The HD locus has been assigned to 4p16.3 distal to the DNA segment D4S10. However, the precise location of this gene is still unknown. At least three regions, together encompassing more than 3.5 Mb of DNA, can still be considered as candidate regions for the HD gene. Our efforts are directed toward the cloning and the complete characterization of one of these regions. Thus far we have cloned 460 kb of DNA in contiguously overlapping cosmids distal to D4S111 and have developed a detailed long-range restriction map orienting the contig within the terminal region of 4p16.3. We characterized 15 CpG-rich islands defined by tightly clustered rare cutter restriction sites for the enzymes NotI, BssHII, EagI, NruI, and SacII. In addition, we show that the sequences associated with the CpG-rich islands detect cross-species conservation. The detailed genetic analysis of the 460-kb contig provides a framework for the identification of genes, which can be assessed for the characteristics expected for the HD gene.

Animals↗
PubMed1997

Regional gene mapping using mixed radiation hybrids and reverse chromosome painting.

We describe a new approach for low-resolution physical mapping using pooled DNA probe from mixed (non-clonal) populations of human-CHO cell hybrids and reverse chromosome painting. This mapping method is based on a process in which the human chromosome fragments bearing a complementing gene were selectively retained in a large non-clonal population of CHO-human hybrid cells during a series of 12- to 15-Gy gamma irradiations each followed by continuous growth selection. The location of the gene could then be identified by reverse chromosome painting on normal human metaphase spreads using biotinylated DNA from this population of "enriched" hybrid cells. We tested the validity of this method by correctly mapping the complementing human HPRT gene, whose location is well established. We then demonstrated the method's usefulness by mapping the chromosome location of a human gene which complemented the defect responsible for the hypersensitivity to ionizing radiation in CHO irs-20 cells. This method represents an efficient alternative to conventional concordance analysis in somatic cell hybrids where detailed chromosome analysis of numerous hybrid clones is necessary. Using this approach, it is possible to localize a gene for which there is no prior sequence or linkage information to a subchromosomal region, thus facilitating association with known mapping landmarks (e.g. RFLP, YAC or STS contigs) for higher-resolution mapping.

Animals↗
PubMed1997

EcoRI restriction fragment-length polymorphism of the human immunoglobulin variable lambda 8 (IGLV8) subgroup reveals a gene family.

The human immunoglobulin lambda locus (IGL) maps on chromosome 22q11.1-q11.2 and directs the synthesis of lambda-type Ig light chains. This locus is formed by three gene clusters (VA, VB and VC) that encompass the variable coding genes and the J-C cluster plus the joining segments and the constant genes. Recently the variable lambda gene clusters were mapped by the contig methodology which located all the known functional v-lambda genes and pseudogenes. The 30 functional v-lambda genes described so far were subgrouped into ten families (V lambda I to V lambda X), but RFLP studies have estimated that the germline repertoire contains about 70 genes. Based on sequence comparisons, we defined specific oligonucleotide primers for the unique IGLV8S1 gene described. The cloned 244 bp product obtained from genomic DNA with these primers was sequenced and used as probe in Southern hybridization EcoRI RFLP analysis of Brazilian people. We detected the IGLV8S1 gene in a 3.7 kb EcoRI restriction fragment present in all the individuals analyzed, in agreement with the physical map of the IGL locus. Moreover, we detected an 8.0 kb EcoRI monomorphic fragment and a 6.0 kb EcoRI polymorphic fragment. These data suggest that the IGLV8 subgroup is a gene family.

Amino Acid Sequence↗
PubMed1997

High-speed positional cloning based on restriction landmark genome scanning.

Restriction landmark genome scanning (RLGS) was developed as a method of genome analysis that is based on the concept that restriction enzyme sites can be used as landmarks. In this article, we demonstrate how this method can be used for the systematic, successful positional cloning of mouse mutant reeler gene. The major advantage of the RLGS method is that it allows the scanning of several thousand spots/loci throughout the genome with one RLGS profile. High-speed positional cloning based on the RLGS method includes (1) high-speed construction of a linkage map (RLGS spot mapping), (2) high-speed detection of RLGS spot markers tightly linked to the mutant phenotype (RLGS spot bombing method), and (3) construction of YAC contigs covering the region where tightly linked spot markers are located (RLGS-based YAC contig mapper). We introduced a series of these procedures by using them to positionally clone the reeler gene. High-speed construction of the whole genetic map and spots/loci (less than 1 cM) within the closest flanking markers is demonstrated. The RLGS-based YAC contig mapper also efficiently yielded the YAC physical contig map of the target region. Finally, we cloned the reeler gene, which is the causal gene for the perturbation of the three-dimensional brain architecture due to the abnormal migration of neuroblasts in reeler mouse. Since the RLGS method itself can be used for any organism, we conclude that the total RLGS-based positional cloning system can be used to identify any mutant gene of any organism.

Animals↗
PubMed1994

Mapping by insertion mutagenesis without cloning.

This paper describes a new strategy for positioning specific loci on known genomic maps or for generating high-resolution physical maps of organisms that are susceptible to transposable elements. The strategy does not require cloning and thus saves time and effort. It is based on isolating cell lines containing appropriate insertions of a DNA element (transposon) carrying a selectable marker and one or more restriction sites. DNA from independent cell lines is digested to completion with a restriction enzyme that cuts within the transposon and the adjacent genomic DNA. The fragments thus produced are analyzed by partial digestions with a panel of restriction enzymes, separated and probed sequentially with oligonucleotides complementary to the ends of the transposon. Algorithms that compare and order the different restriction fingerprints are used to either place the unknown locus on an existing restriction map or, in the case of a new genome, to form contigs to generate a map. The usefulness of this strategy was demonstrated by mapping an Escherichia coli insertion mutation that was difficult to map by more standard procedures.

Algorithms↗
PubMed1996

A 4.3 Mb YAC Contig in Human Xp11.2: Long-Range Restriction Mapping and Identification of CpG Islands.

The Xp11.2 region o the human X chromosome contains genes involved in a number of inherited diseased, with at least one locus that escapes X chromosome inactivation, as well as abnormal methylation polymorphism. We isolated a series of yeast artificial chromosome (YAC) clones by hybridization screening with DNA probes localized within this region and assembled them into a 4.3 Mb contig spanning from Xp11.21 to Xp11.23 by a combination of Alu-PCR fingerprinting, STS-PCR and DNA probe cross hybridization. On the basis of these overlapping YAC clones we have constructed the long-range restriction map of this interval and placed exactly some DNA markers. Four CpG-dense regions between ARAF1 and OATL2 were identified based on the long-range restriction mapping, which indicated the distribution of genes within this interval. It should assist in the future nucleic acid sequence analysis and novel gene identification in this region.

Journal Article↗
PubMed1993

Human tissue factor pathway inhibitor (TFPI) gene: complete genomic structure and localization on the genetic map of chromosome 2q.

Tissue factor pathway inhibitor (TFPI), a protease inhibitor that circulates in association with plasma lipoproteins (VLDL, LDL and HDL), helps to regulate the extrinsic blood coagulation cascade. We have cloned a 125-kb genomic region containing the entire human TFPI gene on six overlapping cosmids and prepared a restriction map of this contig to clarify gene structure. More than half (45 kb) of the 85-kb gene is occupied with 5' noncoding elements: coding begins at exon 3. A HindIII RFLP identified with one cosmid was genotyped in the CEPH panel of 59 reference families. Linkage analysis using markers on human chromosome 2 located the TFPI gene on 2q, 36 cM proximal to D2S43(pYNZ15) and 13 cM distal to the crystalline gamma-polypeptide locus CRYGP1(p5G1).

Base Sequence↗
PubMed2004

The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae.

Cyanidioschyzon merolae is a small unicellular red alga that is considered to belong to one of the most deeply branched taxa in the plant kingdom. Its genome size is estimated to be 16.5 Mbp, one of the smallest among free-living eukaryotes. In the nucleus containing this small genome, one nucleolus is clearly observed, but the molecular basis for the intranuclear structure including ribosomal DNA organization is still unclear. We constructed a bacterial artificial chromosome library for C. merolae 10D composed of two subsets with different insert size distributions. The two subsets have average insert sizes of 97 and 48 kb, representing 10.0- and 6.9-fold genome-equivalent coverage of the haploid genome, respectively. For application to whole-genome shotgun sequencing, the termini of each clone were sequenced as sequence-tagged connectors and mapped on the contigs assigned to chromosomes. Screening for rRNA genes by conventional colony hybridization with high-density filter blots and subsequent sequencing revealed that the C. merolae genome contained the smallest number of ribosomal DNA units among all the eukaryotes examined to date. They consist of only 3 single units of rRNA genes distributed on separate chromosomal loci, representing an implication for concerted evolution. Based on these results, the origin and evolution of the nucleolus are discussed.

Base Sequence↗
PubMed1994

[Physical study of big fragments and search strategy of genes. Application to locus of infant spinal muscular atrophies].

Spinal muscular atrophies (SMA) represent the second most common fatal autosomal recessive disorder after cystic fibrosis. Childhood SMAs are divided into severe (type I) and mild forms (types II and III). By a combination of genetic and physical mapping, a YAC contig of the 5q13 region spanning the disease locus was constructed that showed the presence of low copy-repeats in this region. Allele segregation was analyzed at the closest genetic loci detected by markers C212 and C272 in 201 SMA families. Inherited and de novo deletions were observed in 10 SMA patients. Moreover, deletions were strongly suggested in at least 18% of SMA type I patients by the observation of marked heterozygosity deficiency for the loci studied. These results indicate that deletion events are statistically associated with the severe form of SMA.

Chromosome Mapping↗
PubMed2004

Refinement of the DFNA4 locus to a 1.44 Mb region in 19q13.33.

Many forms of autosomal dominant non-syndromic hearing impairment are known. While the underlying gene defects and causative mutations have been discovered for some forms, the gene responsible for DFNA4 has remained elusive to date. Examination of a German four-generation kindred led to the identification of a 1.44 Mb map segment in contig NT_011109 as being the most likely DFNA4 candidate region in 19q13.33. The recombination breakpoints in this family and the intervals of two previously reported DFNA4 families allowed us to delineate a minimum consensus region between the markers D19S879 and D19S246. In our family, a maximum two-point LOD score of 4.5 was obtained at theta = 0 for the marker D19S867. Within the refined DFNA4 interval the public databases list more than 50 genes, from which several appear to be promising DFNA4 candidates due to similarities with animal models and with other causative genes involved in hearing disability.

Adult↗
PubMed2005

Complexity of the major surface protease (msp) gene organization in Leishmania (Viannia) braziliensis: evolutionary and functional implications.

The major surface protease (msp or gp63) of Leishmania plays a major role in the host-parasite interaction. We analysed here the structure of the msp gene locus in Leishmania (Viannia) braziliensis and compared it to results obtained in other species. Physical mapping of cosmid contigs revealed a minimum of 37 genes per haploid genome and at least 8 different msp gene families. Within the same organism, these genes showed a nucleotide sequence varying in certain stretches from 3 to 34%, and a mosaic structure. From an evolutionary point of view, major differences were observed between subgenera Viannia and Leishmania, both in terms of msp gene number and sequence. Within subgenus Viannia, phenetic analysis revealed three clusters in which sequence variants of L. (Viannia) braziliensis and L. (Viannia) guyanensis were interspersed. Functional implications of our results were explored from predicted L. (Viannia) braziliensis protein sequences: regions encoding the msp catalytic site showed a conserved sequence, while regions encoding surface domains possibly involved in the host-parasite interaction (macrophage adhesion sites and immunodominant B-cell and T-cell epitopes) were variable. We speculate that this would be an adaptive strategy of the parasite.

Animals↗
PubMed2001

The immunoglobulin heavy chain locus of the duck. Genomic organization and expression of D, J, and C region genes.

The region of the duck IgH locus extending from upstream of the proximal diversity (D) segment to downstream of the constant gene cluster has been cloned and mapped. A sequence contig of 48,796 base pairs established that the organization of the genes is D-J(H)-mu-alpha-upsilon. No evidence for a functional homologue (or remnant) of a delta gene was found. The alpha gene is in inverted transcriptional orientation; class switch to IgA expression thus requires inversion of the approximately 27-kilobase pair region that includes both mu and alpha genes. The secreted forms of duck alpha and mu are each encoded by 4 constant region exons, and the hydrophobic C-terminal regions of the membrane receptor forms of alpha and mu are encoded by one and two transmembrane exons, respectively. Putative switch (S) regions were identified for duck mu and upsilon by comparison with chicken Smu and Supsilon sequences and for duck alpha by comparison with mouse Salpha. The duck IgH locus is rich in complex variable number tandem repeats, which occupy approximately 60% of the sequenced region, and occur at a much higher frequency in the IgH locus than in other sequenced regions of the duck genome.

Amino Acid Sequence↗
PubMed1996

Localisation of two candidate genes for mental retardation using a YAC physical map of the Xq21.1-21.2 subbands.

Genetic studies in families with X linked mental retardation have suggested the location of several MR genes in the human q21 region. Since the establishment of cloned resources is an essential step towards the cloning of genes involved in inherited diseases, we built a yeast artificial chromosome (YAC) contig and an STS map of this part of the X chromosome. The contig, which extends from PGK1 in Xq13.3 to DXS1002 in Xq21.2, consists of 30 YACs mapped with 21 markers and spans about 6 Mb. The YAC contig was used as a framework to localise several previously known genes and CEPH/Genethon polymorphic markers, as well as to construct a physical map of the region surrounding one of these genes. We recently localised a presumed MR locus to the region flanked by DXS233 (proximal) and CHM (distal). In the present work, the zinc finger gene, ZNF6, has been shown to lie within this region and to be highly expressed in brain, making it a good candidate MR gene. Similarly the VDAC1 gene has been mapped between DXS986 and DXS72 and its candidate gene status for the Allan-Herndon-Dudley syndrome is discussed.

Base Sequence↗
PubMed2001

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.

Chromosomes, Human, Pair 1↗