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At least 1,063 records · Page 59Linked to original sources
PubMed2006

A second-generation integrated map of the silkworm reveals synteny and conserved gene order between lepidopteran insects.

A second-generation linkage map was constructed for the silkworm, Bombyx mori, focusing on mapping Bombyx sequences appearing in public nucleotide databases and bacterial artificial chromosome (BAC) contigs. A total of 874 BAC contigs containing 5067 clones (22% of the library) were constructed by PCR-based screening with sequence-tagged sites (STSs) derived from whole-genome shotgun (WGS) sequences. A total of 523 BAC contigs, including 342 independent genes registered in public databases and 85 expressed sequence tags (ESTs), were placed onto the linkage map. We found significant synteny and conserved gene order between B. mori and a nymphalid butterfly, Heliconius melpomene, in four linkage groups (LGs), strongly suggesting that using B. mori as a reference for comparative genomics in Lepidotera is highly feasible.

Animals↗
PubMed2004

BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea.

Transposable elements (TEs) are viewed as major contributors to the evolution of fungal genomes. Genomic resources such as BAC libraries are an underutilized resource for studying genome-wide TE distribution. Using the BAC end sequences and physical map that are available for the rice blast fungus, Magnaporthe grisea, we describe a likelihood ratio test designed to identify clustering of TEs in the genome. A significant variation in the distribution of three TEs, MAGGY, MGL, and Pot2 was observed among the fingerprint contigs of the physical map. We utilized a draft sequence of M. grisea chromosome 7 to validate our results and found a similar pattern of clustering. By examining individual BAC end sequences, we found evidence for 11 unique integrations of MAGGY or MGL into Pot2 but no evidence for the reciprocal integration of Pot2 into another TE. This suggests that: (a) the presence of Pot2 in the genome predates that of the other TEs, (b) Pot2 was less transpositionally active than other TEs, or (c) that MAGGY and MGL have integration site preference for Pot2. High transition/transversion mutation ratios as well as bias in transition site context was observed in MAGGY and MGL elements, but not in Pot2 elements. These features are consistent with the effects of a Repeat-Induced Point (RIP) mutation-like process occurring in MAGGY and MGL elements. This study illustrates the general utility of a physical map and BAC end sequences for the study of genome-wide repetitive DNA content and organization.

Chromosomes, Artificial, Bacterial↗
PubMed1999

Physical delineation of a 700-kb region overlapping the Looptail mutation on mouse chromosome 1.

The mouse looptail (Lp) mutation is an established model for neural tube defects with homozygous Lp embryos showing an open neural tube from the caudal midbrain to the tip of the tail. Heterozygous Lp mice are characterized by a "looped-tail" and wobbly head movements. The Lp gene has been mapped to a 0.6-cM interval on mouse chromosome 1 delineated by two clusters of markers, Fcer1gamma/Usf1/D1Mit113/D1Wsu1 on the proximal side and Fcer1alpha/Spna1/D1Mit149 distally. In the present study, we have created a high-resolution physical map of the Lp genetic interval that is based on long-range restriction mapping by PFGE, fluorescence in situ hybridization analysis of interphase nuclei and extended chromatid fibers, and the assembly of a cloned contig. This contig consists of 25 independent and overlapping BAC clones and 3 YAC clones. The combined analysis indicates that the 0.6-cM genetic interval for Lp corresponds to a minimal physical interval of 700 kb that is delineated by D1Mit113 proximally (two crossovers) and Fcer1alpha distally (one crossover). The overall gene order and intergene distances for the region were determined to be D1Mit113-<150 kb-Nhlh1-250 kb-Atp1alpha2-280 kb-Fcer1alpha. Partial sequencing of BAC clones from the contig yielded 42 new STS markers for this region of mouse chromosome 1. Sequence analysis of the BAC clones and assignment of ESTs from the human transcript map to the cloned contig allowed the placement of four new transcription units within this region: Pc326, Kiaa0253, and Pea15 were positioned in the Nhlh1/Atp1alpha2 nonrecombinant interval, while Girk3 was located distal to Atp1alpha2.

Animals↗
PubMed1997

The human guanidinoacetate methyltransferase (GAMT) gene maps to a syntenic region on 19p13.3, homologous to band C of mouse chromosome 10, but GAMT is not mutated in jittery mice.

Guanindinoacetate methyltransferase (gene symbol, GAMT) catalyses the synthesis of creatine from guanidinoacetate and S-adensylmethionine. Pathological mutations in the coding region of GAMT were recently identified in two children with symptoms of muscular hypotonia, ataxia, seizures, and abnormal extrapyramidal movements. During contig construction in the telomeric region of human chromosome 19 we identified a cosmid clone carrying the entire GAMT gene. This clone was shown to overlap with cosmids from a contig that was previously mapped to chromosome 19p13.3. The human GAMT gene has a size of about 5 kb and consists of six exons which agree with the published cDNA sequence. Since the mouse mutations jittery/hesitant are located on band C of mouse chromosome 10 in a region of conserved synteny with 19p13.3 and jittery mice exhibit ataxia and abnormal movement behaviour, the genomic sequence of GAMT was determined in wild-type and jittery mice. The coding region of the GAMT gene, however, was not mutated in these mutant mice. Our linkage and sequence data will facilitate the identification of new GAMT mutations in patients suffering from an abnormal creatine metabolism.

Amino Acid Sequence↗
PubMed1999

A contiguous 3-Mb sequence-ready map in the S3-MX region on 21q22.2 based on high- throughput nonisotopic library screenings.

Progress in complete genomic sequencing of human chromosome 21 relies on the construction of high-quality bacterial clone maps spanning large chromosomal regions. To achieve this goal, we have applied a strategy based on nonradioactive hybridizations to contig building. A contiguous sequence-ready map was constructed in the Down syndrome congenital heart disease (DS-CHD) region in 21q22.2, as a framework for large-scale genomic sequencing and positional candidate gene approach. Contig assembly was performed essentially by high throughput nonisotopic screenings of genomic libraries, prior to clone validation by (1) restriction digest fingerprinting, (2) STS analysis, (3) Southern hybridizations, and (4) FISH analysis. The contig contains a total of 50 STSs, of which 13 were newly isolated. A minimum tiling path (MTP) was subsequently defined that consists of 20 PACs, 2 BACs, and 5 cosmids covering 3 Mb between D21S3 and MX1. Gene distribution in the region includes 9 known genes (c21-LRP, WRB, SH3BGR, HMG14, PCP4, DSCAM, MX2, MX1, and TMPRSS2) and 14 new additional gene signatures consisting of cDNA selection products and ESTs. Forthcoming genomic sequence information will unravel the structural organization of potential candidate genes involved in specific features of Down syndrome pathogenesis.

Chromosome Mapping↗
PubMed1999

Refinement of the RP17 locus for autosomal dominant retinitis pigmentosa, construction of a YAC contig and investigation of the candidate gene retinal fascin.

The RP17 locus for autosomal dominant retinitis pigmentosa has previously been mapped to chromosome 17q by linkage analysis. Two unrelated South African families are linked to this locus and the identification of key recombination events assigned the RP17 locus to a 10 cM interval on 17q22. The work reported here refines the mapping of the locus from a 10 cM to a 1 cM interval between the microsatellite markers D17S1604 and D17S948. A physical map of this interval was constructed using information from the Whitehead/MIT YAC contig WC 17.8. Sequence-tagged site (STS) content mapping of seven overlapping YACs from this contig was employed in order to build the map. A BAC library was screened to cover a gap in the YAC contig and two positive BACs were identified. Intragenic polymorphisms in the retinal fascin gene provided evidence for the exclusion of this candidate as the RP17 disease gene.

Carrier Proteins↗
PubMed1999

A yeast artificial chromosome-based physical map of the juvenile amyotrophic lateral sclerosis (ALS2) critical region on human chromosome 2q33-q34.

The autosomal recessive form of juvenile amyotrophic lateral sclerosis (ALS2; RFALS Type 3) has previously been mapped to the 8-cM interval flanked by D2S115 and D2S155 on human chromosome 2q33-q34. We have established a yeast artificial chromosome (YAC) contig spanning an approximately 8-Mb region of the ALS2 candidate region and mapped 52 transcribed DNA sequences including 13 known genes and 39 expressed sequenced tags within this YAC contig. The establishment of a YAC contig and transcript map that spans the region containing the ALS2 mutation is an essential step in the identification of the ALS2 gene.

Amyotrophic Lateral Sclerosis↗
PubMed2001

A double-deletion mutation in the Pitx3 gene causes arrested lens development in aphakia mice.

The recessive aphakia (ak) mouse mutant is characterized by bilateral microphthalmia due to a failure of lens morphogenesis. We fine-mapped the ak locus to the interval between D19Umi1 and D19Mit9, developed new polymorphic markers, and mapped candidate genes by construction of a BAC contig. The Pitx3 gene, known to be expressed in lens primordia, shows zero recombination with the ak mutation on our intersubspecific intercross panel representing 1170 meioses. A recent report described a deletion in the intergenic region between Gbf1 and Pitx3 as the possible ak mutation. Our results differ in that we find not only the distant intergenic deletion, but also a much larger deletion directly in the Pitx3 gene, eliminating exon 1 and extending into intron 1 and the promoter region. Pitx3 transcript levels are severely reduced in ak/ak mice from E11.5 to newborn (5 +/- 1% of the wildtype levels at E13.5), while an involvement of the flanking Gbf1 and Cig30 genes in the aberrant lens development is highly unlikely based on expression analysis. We conclude that the ak mutation consists of two deletions, the larger of which removes part of Pitx3, indicating a crucial role of this gene in early lens development.

Acetyltransferases↗
PubMed1997

Construction of an approximately 2 Mb contig in the region around 80 cM of Arabidopsis thaliana chromosome 2.

A method for construction of bacterial artificial chromosome (BAC) contigs from a yeast artificial chromosome (YAC) physical map is described. An approximately 2 Mb contig, consisting of two large BAC contigs linked by a small YAC, has been assembled in the region around 80 cM of Arabidopsis thaliana chromosome 2. Clones from this contig will facilitate gene isolation in the region and can be used directly as substrates for DNA sequencing.

Arabidopsis↗
PubMed1998

Isolation of BAC clones spanning the Xq22.3 translocation breakpoint in a lissencephaly patient with a de novo X;2 translocation.

X linked lissencephaly and subcortical band heterotopia (XLIS/SBH) is a disorder of cortical development, which causes classical lissencephaly with severe mental retardation and epilepsy in hemizygous males and SBH associated with milder mental retardation and epilepsy in heterozygous females. Here we report the fine mapping of a breakpoint involved in a de novo X;autosomal balanced translocation (46,XX,t(X;2) (q22.3;p25.1)) previously described in a female with classical lissencephaly. We constructed a complete 490 kb BAC contig around the Xq22.3 breakpoint with 11 novel STSs and isolated three BAC clones spanning the breakpoint. This mapping information and BAC contig will be useful in the detailed characterisation of the XLIS gene and other contiguous genes which may also be involved in brain development or function.

Brain↗
PubMed2001

Three loci on mouse chromosome 6 influence onset and final incidence of type I diabetes in NOD.C3H congenic strains.

The development of insulin-dependent diabetes mellitus in both human and mouse is dependent on the interaction between genetic and environmental factors. The analysis of newly created NOD.C3H congenic strains for spontaneous and cyclophosphamide-induced diabetes has allowed the definition of three controlling genetic loci on mouse chromosome 6. A NOD-derived susceptibility allele at the Idd6 locus strongly influences the onset of diabetes in spontaneous diabetes. A NOD-derived resistance allele at the Idd19 locus affects the final diabetes incidence observed in both models, while a novel locus, provisionally termed Idd20, appears to control Idd19 in an epistatic manner. Decreased diabetes incidence is observed in CY-induced diabetes when Idd20 is homozygous for the C3H allele, while heterozygosity is associated with an increase in diabetes incidence. The Idd20, Idd19, and Idd6 candidate regions fall respectively within genetically defined intervals of 4, 7, and 4.5 cM on mouse chromosome 6. From our YAC contig, Idd6 would appear to localize within a ca. 1.5-Mb region on distal chromosome 6.

Age Factors↗
PubMed2002

A three-megabase yeast artificial chromosome contig spanning the C57BL mouse Igh locus.

The mouse Ig H chain (Igh) complex locus is composed of >100 gene segments encoding the variable, diversity, joining, and constant portions of the Ab H chain protein. To advance the characterization of this locus and to identify all the V(H) genes, we have isolated the entire region from C57BL/6 and C57BL/10 as a yeast artificial chromosome contig. The mouse Igh locus extends approximately three megabases and contains at least 134 V(H) genes classified in 15 partially interspersed families. Two non-Igh pseudogenes (Odc-rs8 and Rpl32-rs14) were localized in the distal part of the locus. This physical yeast artificial chromosome map will provide important structure and guidance for the sequencing of this large, complex, and highly repetitive locus.

Animals↗
PubMed1990

Yeast artificial chromosomes: tools for mapping and analysis of complex genomes.

Libraries of yeast artificial chromosomes (YACs) are representative of complex genomes, and typical YACs contain single fragments of DNA that are up to a megabase or more in size, are stable during growth, and are faithful to genomic DNA. Such YACs may permit (1) the use of complete gene units for a number of research and medical purposes; and (2) the assembly of chromosome-sized contigs in a single map that unifies genetic and physical data.

Animals↗
PubMed1997

Physical mapping of two histone gene clusters on human chromosome 6p22.1-22.2.

Histones are basic proteins which are responsible for the assembly and maintenance of the nucleosomal structure within the chromosomal fiber in eukaryotes. Two clusters of these genes have previously been mapped to the region 6p21.1-p22.2. We describe here a radiation hybrid map, a long range restriction map and a YAC contig covering and linking these two clusters and giving the precise localisation with respect to the HLA complex. The large cluster contains five H1 histone genes in the 6p22.2 region, the smaller only one, H1F5 (H1.5), in 6p22.1. In both clusters, each H1 locus is accompanied by several core histone genes. The large cluster has additionally been covered by a sequence ready PAC contig and three probably unrelated genes (TRMI2, BTN and SSADH) have been accurately localized within the 6p22.2-p22.1 region.

Chromosomes, Human, Pair 6↗
PubMed1993

A contig of non-chimaeric YACs containing the spinal muscular atrophy gene in 5q13.

We have constructed a contig of non-chimaeric yeast artificial chromosomes (YACs) across the candidate region for childhood autosomal recessive spinal muscular atrophy (SMA) in 5q13. A novel microsatellite reduces the candidate region to approximately 400kb of DNA distal to D5S435. The candidate region contains blocks of chromosome 5 specific repeats which have copies on 5p as well as elsewhere on 5q. Restriction mapping of the YACs reveals at least one CpG island in the SMA gene region. The YAC maps indicate that the contig contains minimal rearrangements or deletions. The data show the value of screening several YAC libraries simultaneously in order to construct a set of overlapping sequences suitable for candidate gene searches and direct genomic sequencing.

Base Sequence↗
PubMed1994

High resolution mapping of overlapping cosmids by fluorescence in situ hybridization.

The constituents of two cosmid contigs were analyzed by high resolution mapping using two-color fluorescence in situ hybridization (FISH) to extended DNA molecules. Samples were prepared by lysing the nuclei in situ followed by histone depletion. This treatment results in elongate DNA filaments appropriate for high resolution mapping. The hybridization signals appeared as a strong of fluorescent spots separated by non-fluorescing gaps. Probe-specific features of the hybridization patterns were detected and some of the non-fluorescing gaps were found to represent regions of repetitive DNA suppressed during hybridization.

Amnion↗
PubMed1999

A radiation hybrid map of 48 loci including the clouston hidrotic ectodermal dysplasia locus in the pericentromeric region of chromosome 13q.

To facilitate the identification of the gene responsible for Clouston hidrotic ectodermal dysplasia (HED), we used a chromosome 13-specific radiation hybrid panel to map 54 loci in the HED candidate region. The marker retention data were analyzed using RHMAP version 3. The 54 markers have an average retention frequency of 31.6% with decreasing retention as a function of distance from the centromere. Two-point analysis identified three linkage groups with a threshold lod score of 4.00; one linkage group consisted of 49 loci including the centromeric marker D13Z1 and the telomeric flanking marker for the HED candidate region D13S143. Assuming a centromeric retention model, multipoint maximum likelihood analysis of these 49 loci except D13Z1 provided a 1000:1 framework map ordering 29 loci with 21 unique map positions and approximately 2000 times more likely than the next order. Loci that could not be ordered with this level of support were positioned within a range of adjacent intervals. This map spans 347 cR9000, has an average resolution of 17.3 cR9000, and includes 3 genes (TUBA2, GJbeta2, and FGF-9), 18 ESTs, 19 polymorphic loci, and 8 single-copy DNA segments. Comparison of our RH map to a YAC contig showed an inconsistency in order involving a reversed interval of 6 loci. Fiber-FISH and FISH on interphase nuclei analyses with PACs isolated from this region supported our order. We also describe the isolation of 8 new chromosome 13q polymorphic (CA)n markers that have an average PIC value of 0.67. These data and mapping reagents will facilitate the isolation of disease genes from this region.

Chromosomes, Human, Pair 13↗
PubMed1993

A physical map of 15 loci on human chromosome 5q23-q33 by two-color fluorescence in situ hybridization.

The q23-q33 region of human chromosome 5 encodes a large number of growth factors, growth factor receptors, and hormone/neurotransmitter receptors. This is also the general region into which several disease genes have been mapped, including diastrophic dysplasia, Treacher Collins syndrome, hereditary startle disease, the myeloid disorders that are associated with the 5q-syndrome, autosomal-dominant forms of hereditary deafness, and limb girdle muscular dystrophy. We have developed a framework physical map of this region using cosmid clones isolated from the Los Alamos arrayed chromosome 5-specific library. Entry points into this library included 14 probes to genes within this interval and one anonymous polymorphic marker locus. A physical map has been constructed using fluorescence in situ hybridization of these cosmids on metaphase and interphase chromosomes, and this is in good agreement with the radiation hybrid map of the region. The derived order of loci across the region is cen-IL4-IL5-IRF1-IL3-IL9-EGR1-CD1 4-FGFA-GRL-D5S207-ADRB2-SPARC-RPS14+ ++-CSF1R- ADRA1, and the total distance spanned by these loci is approximately 15 Mb. The framework map, genomic clones, and contig expansion within 5q23-q33 should provide valuable resources for the eventual isolation of the clinically relevant loci that reside in this region.

Chromosome Mapping↗