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PubMed2003

[Localization of genes, determining quantitative traits in wheat: amendment to the "catalog of chromosomal mapping of genes in domestic cultivars of wheat"].

An amendment to the catalog of chromosome location of genes in Russian wheat cultivars was constructed with the published data of the recent decade. The results of chromosomal localization were summarized and analyzed by methods of multivariate statistics. Chromosomes critical for 40 quantitative traits under study proved to cluster according to their homeology, i.e., by homeological groups. The hypotheses providing an explanation for this finding are considered. It is suggested that quantitative traits are similarly controlled by genes located on homeological chromosomes in common wheat, making it possible to isolate a limited number of major genes for each particular quantitative trait.

Chromosome Mapping↗

PubMed1997

Cloning and chromosome mapping of the feline genes p21WAF1 and p27Kip1.

For investigation of the relation of cell cycle regulation with tumorigenesis in cats, we carried out molecular cloning of feline p21WAF1 and p27Kip1 cDNAs and chromosomal mapping of these genes on the cat genome. The feline p21WAF1 cDNA clone obtained in this study encoded 164 amino acids (aa) showing 83.5% and 76.8% sequence similarity with those of the human and mouse counterparts, respectively. The cat p27Kip1 cDNA clone isolated here encoded 198 aa, showing sequence similarities of 93.4% and 90.4% with its human and mouse counterparts, respectively. Using a panel of feline x rodent somatic cell hybrids, the feline CDKN1A (p21WAF1) and CDKN1B (p27Kip1) loci were assigned to feline chromosomes B2 and B4, respectively. Southern-blot analyses of 17 feline spontaneous leukemia and lymphoma cases using these cDNAs as probes did not reveal any rearrangements in either the p21WAF1 or the p27Kip1 gene. RT-PCR/SSCP (single strand conformation polymorphism) analysis of p27Kip1 cDNA did not uncover any amino acid substitutions in the 10 feline leukemia and lymphoma cases that were examined.

Amino Acid Sequence↗

PubMed1997

X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content.

A YAC/STS map of the X chromosome has reached an inter-STS resolution of 75 kb. The map density is sufficient to provide YACs or other large-insert clones that are cross-validated as sequencing substrates across the chromosome. Marker density also permits estimates of regional gene content and a detailed comparison of genetic and physical map distances. Five regions are detected with relatively high G + C, correlated with gene richness; and a 17-Mb region with very low recombination is revealed between the Xq13.3 [XIST] and Xq21.3 XY homology loci.

Base Composition↗

PubMed1997

Prevalence and chromosomal map location of Staphylococcus aureus adhesin genes.

Using genomic DNA from 25 unrelated strains and probes specific for each gene, we assessed the prevalence of the Staphylococcus aureus (Sa) adhesion genes cna, fnbA, fnbB, fib, clfA, fbpA, ebpS and map. All 25 strains encoded fib, clfA, ebpS, map and at least one of the fnb genes. fbpA and coa appeared to be allelic variants of the same gene with the fbpA variant being present in only four of 25 isolates. cna was present in 10 of 25 strains. Using Southern blot analysis of SmaI-digested genomic DNA resolved by pulsed-field gel electrophoresis, the adhesion genes were mapped to SmaI fragments A (ebpS), B (fib and clfA), C (fnbA/fnbB), E (fbpA), F (map) and G (cna). Despite variations in SmaI restriction profiles, co-localization of adhesin genes with genes known to map to specific SmaI fragments in the Sa 8325-4 chromosome strains suggests that the chromosomal location of each adhesin gene is conserved.

Adhesins, Bacterial↗

PubMed1995

Isolation of the human peroxisome proliferator activated receptor gamma cDNA: expression in hematopoietic cells and chromosomal mapping.

The nuclear receptor superfamily of transcription factors, which includes the retinoic acid receptors and v-erb A, play important roles in the molecular control of hematopoiesis. To identify nuclear receptors expressed in hematopoietic cells, we screened a human bone marrow cDNA library using a degenerate oligonucleotide and isolated a 1.85-kb full-length cDNA encoding a new human member of this superfamily, the peroxisome proliferator activated receptor gamma (hPPAR gamma). Two different hPPAR gamma transcripts were expressed in hematopoietic cells: a 1.85-kb transcript, which corresponds to the full-length mRNA (PPAR gamma 1), and a 0.65-kb transcript (PPAR gamma 2), which cannot encode all of the nuclear receptor functional domains. Normal neutrophils and peripheral blood lymphocytes, as well as circulating leukemic cells from patients with AML, ALL, and CML, express only PPAR gamma 2 on Northern blot analysis. In contrast, only the PPAR gamma 1 transcript was detected in a variety of human leukemia cell lines and in cultured normal primary bone marrow stromal cells. Both transcripts were detected in various fetal and adult nonhematopoietic tissues. We mapped the location of the hPPAR gamma gene to human chromosome 3p25 by somatic cell hybridization and linkage analysis. PPARs have been shown to be activated by peroxisome proliferating agents, long-chain fatty acids and arachidonic acid. Human PPAR gamma, although homologous to the PPAR gamma s of other species, has unique sequence and amino acid differences. Identification of hPPAR gamma will allow further understanding of its role in human cellular leukotriene, prostaglandin, and peroxide degradative or synthetic pathways, as well as its role in lipid metabolism and regulation of adipocyte differentiation.

Adult↗

PubMed2000

Gene structure and chromosomal mapping of the rat smooth muscle calponin gene.

Smooth muscle cells (SMC) express a battery of lineage-restricted genes whose encoded proteins impart the unique contractile phenotype that characterizes this muscle type. While the encoded function of many SMC-restricted genes has been extensively analyzed, less is known about their position within the genome and the regulatory factors governing their transcription. In this report, we define the gene structure, 5' promoter analysis, and chromosomal mapping of the rat smooth muscle calponin (CnnI) gene. The rat CnnI gene is comprised of seven exons spanning approximately 8 kb of genomic sequence. The intron-exon boundaries of the rat CnnI gene match precisely those in human and mouse. Primer extension and RNase protection assays indicate two major transcription start positions (tsp). Comparative sequence analysis of the 5' promoter region reveals several conserved cis regulatory elements, including a TA-rich element within 30 nt of the tsp that could be a recognition site for TATA-binding protein and two CCAAT boxes. Transient and stable transfection studies support the hypothesis that distal regulatory elements confer SMC-restricted expression of CnnI. Finally, using an F2 intercross, we have mapped the rat CnnI gene to the telomeric end of Chromosome (Chr) 8. These studies provide additional information relating to the control of CnnI gene expression and provide a platform to begin assessing the potential linkage of CnnI to spontaneous and experimental disease phenotypes in rats.

Animals↗

PubMed1997

Chromosomal mapping of the gene encoding serotonin N-acetyltransferase to rat chromosome 10q32.3 and mouse chromosome 11E2.

Pineal melatonin is produced during the night. Its nocturnal increase regulates circadian rhythms and the photoperiodic reproductive response. Serotonin is acetylated to N-acetylserotonin by serotonin N-acetyltransferase (SNAT) and then methylated to form melatonin by hydroxyindole-O-methyltransferase (HIOMT). The rhythmicity of melatonin synthesis is regulated by the rhythmic activity of SNAT. Most laboratory mice do not have melatonin because of a genetic defect in the activity of SNAT and/or HIOMT. In a previous study using a recombinant inbred strain, we have found that the locus controlling pineal SNAT activity (Nat4) is located on mouse Chromosome 11. Recently, SNAT has been cloned in the rat. In the present study, the gene encoding SNAT was localized, using a rat cDNA fragment, on rat and mouse chromosomes by direct R-banding fluorescence in situ hybridization (FISH). In addition, using molecular linkage analysis with interspecific backcross mice, a gene encoding SNAT was mapped on a mouse chromosome. The gene encoding SNAT was localized to rat chromosome 10q32.3 and mouse Chromosome 11E2 by FISH. The molecular linkage analysis demonstrated that the gene encoding SNAT maps 1.5 cM distal to D11Mit11. The data suggest that Nat4 encodes SNAT. These chromosomal locations are in a region of conserved linkage homology between the two species.

Animals↗

PubMed1998

Identification and sequence analysis of a 27-kilobase chromosomal fragment containing a Salmonella pathogenicity island located at 92 minutes on the chromosome map of Salmonella enterica serovar typhimurium LT2.

Using a genomic approach, we have identified a new Salmonella pathogenicity island, SPI-4, which is the fourth Salmonella pathogenicity island to be identified. SPI-4 was located at 92 min on the chromosome map and was flanked by the ssb and soxSR loci. The DNA sequence covering the entire SPI-4 and both boundaries was determined. The size of SPI-4 was about 25 kb and it contains 18 putative open reading frames (ORFs). Three of these ORFs encode proteins that have significant homology with proteins involved in toxin secretion. Another five ORFs encode proteins that have significant homology with hypothetical proteins from Synechocystis sp. strain PCC6803 or Acinetobacter calcoaceticus. The rest of the ORFs encode novel proteins, one of which has five membrane-spanning domains. SPI-4 is likely to carry a type I secretion system involved in toxin secretion. Furthermore, a previously identified locus (ims98), which is required for intramacrophage survival, was also mapped within the SPI-4 region. These findings suggested that SPI-4 is needed for intramacrophage survival.

Amino Acid Sequence↗

PubMed2002

cDNA cloning, genomic structure and chromosomal mapping of the mouse glucuronyltransferase-S involved in the biosynthesis of the HNK-1 carbohydrate epitope.

The HNK-1 carbohydrate epitope is expressed on a series of cell adhesion molecules and some glycolipids in the nervous system. Two glucuronyltransferases (GlcAT-P and GlcAT-S) are involved in the biosynthesis of the HNK-1 carbohydrate epitope. In this study, we isolated cDNA and genomic clones encoding the mouse glucuronyltransferase-S involved in the biosynthesis of the HNK-1 carbohydrate epitope and determined the structural organization of the gene. The deduced amino acid sequence of mouse GlcAT-S consists of 324 amino acids and has a type II membrane topology. The predicted amino acid sequence of mouse GlcAT-S is 98.1% identical to that of rat GlcAT-S. Northern blot analysis revealed that the mouse GlcAT-S transcript is specifically expressed in the nervous system. Moreover, the mouse GlcAT-S gene is composed of four exons spanning over more than 25 kilobase pairs. Southern blot analysis and chromosomal mapping indicated that the mouse GlcAT-S gene is a single copy gene and it was mapped to the A4-B region of mouse chromosome 1.

5' Flanking Region↗

PubMed1994

Chromosomal mapping of mouse 5S rRNA genes by direct R-banding fluorescence in situ hybridization.

The mouse 5S rRNA gene was mapped by direct R-banding fluorescence in situ hybridization (FISH) with biotinylated probes. Two genomic fragments amplified by PCR from total genomic DNA of BALB/c mice and Mus spretus, a 0.16-kb fragment that included the 121-bp 5S rRNA gene and a 1.6-kb fragment that included the whole spacer region, were used for chromosomal mapping of the 5S rRNA gene. Both fragments hybridized to a single locus on a pair of autosomal chromosomes of BALB/c mice. The major cluster of mouse 5S rRNA genes was assigned to the most terminal R-negative to R-positive bands of the E region of mouse Chromosome 8, which is homologous to the linkage of the 5S rRNA gene on the long arm of human chromosome 1. The location of the 5S rRNA gene was mapped in five laboratory strains, in wild mice of six Mus musculus subspecies (domesticus, brevirostris, musculus, bactrianus, castaneus, and molossinus) derived from 10 separate localities, and in four different Mus species (spretus, hortulanus, spicilegus, and caroli), using FISH. The 5S rRNA cluster mapped to the same position on the chromosomes of all mouse species and subspecies studied. These results suggest that the location of the mouse 5S rRNA gene on the distal telomeric region of Chromosome 8 is evolutionarily conserved. In comparison, the chromosomal assignments of centromeric 18S-28S rRNA genes are highly variable among the different M. musculus subspecies and Mus species.

Animals↗

PubMed1996

Physical and genetic chromosomal map of an M type 1 strain of Streptococcus pyogenes.

A physical map of the chromosome of an M type 1 strain of Streptococcus pyogenes was constructed following digestion with three different restriction enzymes, SmaI, SfiI, and SgrAI, and separation and analysis of fragments by pulsed-field gel electrophoresis. The genome size of this strain was estimated to be 1,920 kb. By employing Southern hybridization and PCR analysis, 36 genes were located on the map.

Electrophoresis, Gel, Pulsed-Field↗

PubMed1992

Characterization and chromosomal mapping of the gene encoding the cellular DNA binding protein HTLF.

A region of the human T-cell leukemia virus long terminal repeat (HTLV-I LTR) located between -155 and -117 is important in the regulation of gene expression by the ets family of transcription factors. In an attempt to identify additional cellular transcription factors that bind to this portion of the HTLV-I LTR, we used lambda gt11 expression cloning with oligonucleotides corresponding to this element. A 1239-bp cDNA was isolated from a Jurkat cDNA library, which encoded a protein capable of binding to this purine-rich region. This protein, which we designated human T-cell leukemia virus enhancer factor (HTLF), contains a domain with homology to the recently described fork head DNA binding domain. Chromosome mapping of the HTLF gene demonstrated that it was localized to human chromosome 2p16-p22. HTLF is a unique cellular gene that may function in the transcriptional regulation of HTLV-I LTR.

Amino Acid Sequence↗

PubMed1997

Molecular cloning, chromosomal mapping and developmental expression of BAPX1, a novel human homeobox-containing gene homologous to Drosophila bagpipe.

We describe here the cloning of the human BAPX1 gene, a homologue of the Drosophila bagpipe gene which has 87% aa identity within the homeodomain relative to the fly gene. We recently have identified the murine bagpipe homolog. The predicted aa sequence of the human gene has 85% overall identity to the murine gene, with 100% identity in the homeodomain. In mouse, this gene maps to the proximal portion of chromosome 5. We show that the human gene maps to 4p16.1, the human region syntenic with mouse chromosome 5. Expression of BAPX1 was evaluated during human embryonic development by RT-PCR analysis and by RNA in situ hybridization. RT-PCR analysis showed that BAPX1 is expressed in embryo tissues, particularly the limb, and at a lower level in an embryonic lung cell line. RNA in situ hybridization revealed that BAPX1 is predominantly expressed in mesenchymal condensations of the fetal limb and axial skeleton, and in lateral plate mesoderm giving rise to visceral muscle. The expression pattern of BAPX1 combined with the chromosomal localization to 4p16.1, where several human genetic diseases involving dysmorphology of the skeleton have been assigned, raises the potential of it being a candidate gene for one of these disorders. O

Animals↗

PubMed1992

Four novel members of the connexin family of gap junction proteins. Molecular cloning, expression, and chromosome mapping.

We have used low stringency hybridization and polymerase chain reaction (PCR) amplification with degenerate oligonucleotides to identify four new members of the rat connexin gene family. On the basis of their predicted molecular mass, these proteins have been designated connexin (Cx) 40 (Cx40), Cx37, Cx33, and Cx31.1. The new connexins exhibit all of the conserved structural features of the connexin family, including highly similar extracellular and transmembrane domains but divergent major cytoplasmic domains. On the basis of primary sequence similarity, the connexin family may be divided into two classes. Cx40, Cx37, and Cx33 are similar to the previously characterized Cx43 and Cx46. Cx31.1 is similar to Cx26, Cx31, and Cx32. Cx37 and Cx40 mRNAs are expressed in a wide variety of adult organs and tissues, with particular abundance in lung. However, their relative levels are different in many organs and thus their distribution is not completely coincident. Cx33 and Cx31.1 genes exhibit a much more restricted pattern of expression; mRNAs are detected only in testes and skin, respectively. Chromosomal mapping studies indicate that Cx26 and Cx46 are tightly linked on chromosome 14, and Cx37 and Cx31.1 are linked on chromosome 4, while the rest of the connexin genes are dispersed.

Amino Acid Sequence↗

PubMed1996

Chromosome mapping of human (ZNF179), mouse, and rat genes for brain finger protein (bfp), a member of the RING finger family.

The bfp, a member of the RING finger family, has been shown to be predominantly expressed in brain and up-regulated in neural differentiation of P19 embryonic carcinoma cells. Chromosome mapping of the bfp gene by fluorescence in situ hybridization reveals that human BFP (ZNF179) is located at 17p11.2, mouse Bfp at 11B1.3, and rat BFP at 10q22. These results provide additional evidence that the mouse 11B region displays conserved linkage homology with the 17p11.2 region of the human genome and the 10q22 region of the rate genome.

Amino Acid Sequence↗

PubMed1986

Chromosomal map position of genes encoding P adhesins in uropathogenic Escherichia coli.

Escherichia coli isolates from upper urinary tract infections frequently express adherence to human uroepithelium and D-mannose-resistant hemagglutination of human erythrocytes. Such adherence is usually associated with P pili encoded by the pap operon(s). In this paper, we report approximate chromosomal map positions for two copies of the pap operon. Only one copy expressed an adhesin capable of D-mannose-resistant hemagglutination, although both expressed P-related antigen.

Adhesins, Escherichia coli↗

PubMed1995

[Conversion of zinc finger protein to artificial site-specific nuclease: application to chromosome mapping and sequencing].

Zinc finger motif is a novel DNA binding motif characterized by the unique role of zinc; the protein folding and the DNA binding ability are governed by the coordination of a zinc ion. In C2H2-type zinc finger, two cysteines and two histidines contribute to form a globular domain through zinc coordination. The zinc finger of C2H2-type gives promise of recognition for any DNA sequences because of its recognition mode. A C2H2-type zinc finger protein Sp1 has been converted into artificial site-specific nuclease with an attached Ni-based DNA cleavage unit (Gly-Gly-His). This protein cleaved DNA at a single site near the Sp1 recognition sequence. The zinc finger-based nuclease is applicable to chromosome mapping and sequencing.

Base Sequence↗

PubMed2000

Cloning, chromosome mapping and functional characterization of a human homologue of murine gtse-1 (B99) gene.

Murine Gtse-1 (G(2) and S phase expressed protein), previously named B99, is a wt-p53 inducible gene that encodes a microtubule-localized protein which is able to induce G(2)/M phase accumulation when ectopically expressed. Here we report the cloning and characterization of a new cDNA (GTSE-1) encoding a human homologue of the mouse Gtse-1 protein. Chromosome mapping of mouse and human genes assigned Gtse-1 to chromosome 15 and GTSE-1 to chromosome 22q13.2-q13.3 in a region with conserved synteny to that where Gtse-1 mapped. Analysis of the genomic structure revealed that GTSE-1 contains at least 11 exons and 10 introns, spanning approximately 33kb of genomic DNA. Similar to murine Gtse-1, the product of GTSE-1 localized to the microtubules, was able to delay G(2)/M progression when ectopically expressed and was cell cycle regulated. Taken together, these results indicate GTSE-1 as the human functional homologue of murine Gtse-1.

Amino Acid Sequence↗