Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “CHROMOSOME 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 829 records · Page 46Linked to original sources
PubMed1999

Genomic structure, chromosomal mapping, and promoter region analysis of murine uridine phosphorylase gene.

Uridine phosphorylase (UPase) plays an important role in the activation of 5-fluorouracil and in the regulation of tissue and plasma concentration of uridine, a potential biochemical modulator of 5-fluorouracil therapy. UPase expression is affected by the c-H-ras oncogene and various cytokines through unknown mechanisms. To understand its expression and regulation, we cloned the murine UPase gene, defined its genomic organization, determined its 5'- and 3'-end flanking sequences, and evaluated the promoter activity. The UPase gene contains nine exons and eight introns, spanning a total of approximately 18.0 kb. Its promoter lacks canonical TATA and CCAAT boxes, although a CAATAAAAA TATA-like box is seen from -41 to -49. Furthermore, IFN regulatory factor 1, c/v-Myb, and p53 binding sites are present in the promoter region, indicating that UPase expression may be directly regulated by cytokines and oncogene products. The 1.2-kb flanking fragment showed promoter activity driving the expression of the luciferase gene in various mammalian cells. A TGGGG repeat sequence is seen in the 3'-end flanking region. This element is considered to be a potential recombination consensus hot spot that may contribute to the encoding of different UPase isoforms present in different tissues, both normal and neoplastic.

3' Untranslated Regions↗
PubMed1998

Isolation, structural characterization, and chromosomal mapping of the mouse vascular adhesion protein-1 gene and promoter.

Vascular adhesion protein-1 (VAP-1) is an endothelial cell adhesion molecule which mediates lymphocyte binding to endothelial cells. The cloning of a mouse VAP-1 (mVAP-1) cDNA revealed that mVAP-1 is a novel 110/220 kDa transmembrane molecule with significant identity to copper-containing amine oxidases. In this work the nucleotide sequence and primary structure of the mVAP-1 gene was determined and the promoter region was structurally characterized. The isolated approximately 14.4-kb mVAP-1 gene consists of 4 exons and 3 introns. Primer extension analysis and 5' rapid amplification of cDNA ends revealed multiple transcription initiation sites in different tissues suggesting that the mVAP-1 transcription is differently regulated in different tissues. Analysis of the sequence immediately upstream of the detected transcription initiation sites showed no canonical TATA or CCAAT elements, but putative regulatory elements were found close to the detected transcription start sites. The cloning of the mVAP-1 gene reveals the first insight into the genomic organization of murine amine oxidases and will, by targeted disruption of the gene, allow us to understand better the importance of VAP-1 in leukocyte trafficking and monoamine oxidase activity for the function of the immune system.

Amine Oxidase (Copper-Containing)↗
PubMed2004

Molecular cloning, chromosomal mapping, and characteristic expression in tooth organ of rat and mouse Krox-25.

A novel member of the Krox family of proteins, designated Krox-25, was identified by screening clones from the cDNA libraries of a rat incisor and mouse embryo craniofacial tissue. Rat and mouse Krox-25 mRNAs are about 2.4 kb long, encoding 225 and 224 amino acids, respectively. Krox-25 consists of five zinc finger motifs homologous to the Drosophila Krüppel segmentation gene and also contains several consensus amino acid sequences for a protein kinase C binding domain. Northern blot analysis revealed an intense expression of Krox-25 mRNA in rat and mouse teeth, although it was expressed weakly in other tissues, including calvaria, brain, lung, thymus, kidney, and submandibular gland of mouse. In situ hybridization showed that Krox-25 mRNA began to be expressed weakly in the early odontogenic mesenchyme and primitive enamel epithelium located at the apical end of the rat incisor, and Krox-25 expression increased in the presecretory ameloblasts and became intense in the secretory ameloblasts. This expression was also similar to the results of immunohistochemistry and Western blot, especially the Krox-25 localization in the nuclei of enamel epithelial cells. These results suggest that Krox-25 plays an important role as a transcription factor for the cytodifferentiation and amelogenesis of enamel epithelium.

Animals↗
PubMed2025

Phylogeny, chromosomal mapping and expression analyses of wheat CLAVATA pathway components suggest differential selection on receptor-like kinases, CLEs and T3 WOXes.

Ensuring continuous global food security is a major challenge of the 21st century. Wheat contributes approximately 20% of the total calories consumed by humans, and an estimated 60% increase in production will be required by 2050 to meet forecast global demand. In cereals like wheat, inflorescence (ear) size and branching patterns determine the number of flowers (florets) and grains produced, and these aspects of plant architecture are regulated by the activity of stem cells in the growing shoot tips. CLAVATA peptide and receptor-like kinase signalling regulates angiosperm stem cell activity, and as changes in CLAVATA function can improve crop yields, CLAVATA is a key target for reverse engineering. Here, we identify components of the wheat CLAVATA pathway using genome searches against Triticum aestivum and its wild relatives Triticum turgidum ssp. durum, Triticum turgidum ssp. dicoccoides, Triticum urartu and Aegilops tauschii. Using phylogenetic and synteny analysis, we determine the relationship between homoeologues and infer patterns of gene family evolution. Whilst CLAVATA1, BARELY ANY MERISTEM, RECEPTOR-LIKE PROTEIN KINASE 2, CORYNE and CLAVATA2 receptor-like kinase homologues are mainly present as single genome copies as in other grasses, CLAVATA3-like but not TRACHEARY ELEMENT DIFFERENTIATION FACTOR (TDIF)-like peptide encoding genes and WUSCHEL-LIKE HOMEOBOX (WOX) genes have expanded copy numbers with many gene gains and losses during evolution. Our results highlight wheat CLAVATA pathway components for reverse genetic analysis and indicate potential differential selection on wheat receptor-like kinases, their peptide ligands and WOXes.

Triticum↗
PubMed1999

Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping.

As currently being performed with an increasing number of superfamilies, a standardized gene nomenclature system is proposed here, based on divergent evolution, using multiple alignment analysis of all 86 eukaryotic aldehyde dehydrogenase (ALDH) amino-acid sequences known at this time. The ALDHs represent a superfamily of NAD(P)(+)-dependent enzymes having similar primary structures that oxidize a wide spectrum of endogenous and exogenous aliphatic and aromatic aldehydes. To date, a total of 54 animal, 15 plant, 14 yeast, and three fungal ALDH genes or cDNAs have been sequenced. These ALDHs can be divided into a total of 18 families (comprising 37 subfamilies), and all nonhuman ALDH genes are named here after the established human ALDH genes, when possible. An ALDH protein from one gene family is defined as having approximately < or = 40% amino-acid identity to that from another family. Two members of the same subfamily exhibit approximately > or = 60% amino-acid identity and are expected to be located at the same subchromosomal site. For naming each gene, it is proposed that the root symbol 'ALDH' denoting 'aldehyde dehydrogenase' be followed by an Arabic number representing the family and, when needed, a letter designating the subfamily and an Arabic number denoting the individual gene within the subfamily; all letters are capitalized in all mammals except mouse and fruit fly, e.g. 'human ALDH3A1 (mouse, Drosophila Aldh3a1).' It is suggested that the Human Gene Nomenclature Guidelines (http://++www.gene.ucl.ac.uk/nomenclature/guidelines.h tml) be used for all species other than mouse and Drosophila. Following these guidelines, the gene is italicized, whereas the corresponding cDNA, mRNA, protein or enzyme activity is written with upper-case letters and without italics, e.g. 'human, mouse or Drosophila ALDH3A1 cDNA, mRNA, or activity'. If an orthologous gene between species cannot be identified with certainty, sequential naming of these genes will be carried out in chronological order as they are reported to us. In addition, 20 human ALDH variant alleles that have been reported to date are listed herein and are recommended to be given numbers (or a number plus a capital letter) following an asterisk (e.g. 'ALDH3A2*2, ALDH2*4C'). It is anticipated that this eukaryotic ALDH gene nomenclature system will be extended to include bacterial genes within the next 2 years and that this nomenclature system will require updating on a regular basis; an ALDH Web site has been established for this purpose (http://++www.uchsc.edu/sp./sp./alcdbase/a ldhcov.html) and will serve as a medium for interaction amongst colleagues in this field.

Aldehyde Dehydrogenase↗
PubMed1990

Genetic analysis of amdS transformants of Aspergillus niger and their use in chromosome mapping.

The Aspergillus nidulans gene coding for acetamidase (amdS) was introduced into A. niger by transformation. Twelve Amd+ transformants were analysed genetically. The amdS inserts were located in seven different linkage groups. In each transformant the plasmid was integrated in only a single chromosome. Our (non-transformed) A. niger strains do not grow on acetamide and are more resistant to fluoroacetamide than the transformants. Diploids hemizygous for the amdS insert have the Amd+ phenotype. We exploited the opportunity for two-way selection in A. niger: transformants can be isolated based on the Amd+ phenotype, whereas counter-selection can be performed using resistance to fluoroacetamide. On this basis we studied the phenotypic stability of the heterologous amdS gene in A. niger transformants as well as in diploids. Furthermore, we mapped the plasmid insert of transformant AT1 to the right arm of chromosome VI between pabA1 and cnxA1, providing evidence for a single transformational insert. The results also show that the amdS transformants of A. niger can be used to localize non-selectable recessive markers and that the method meets the prerequisites for efficient mitotic mapping. We suggest the use of amdS transformants for mitotic gene mapping in other fungi.

Amidohydrolases↗
PubMed1999

Molecular cloning and chromosomal mapping of the human homologue of MYB binding protein (P160) 1A (MYBBP1A) to 17p13.3.

We have previously isolated and characterized murine MYB binding protein (p160) 1a, a protein that specifically interacts with the leucine zipper motif within the negative regulatory domain of the c-Myb proto-oncoprotein. We now describe the molecular cloning of the human MYBBP1A cDNA and chromosomal localization to 17p13.3 by fluorescence in situ hybridization analysis. Given the likely presence of a tumor suppressor gene (or genes) within this region of chromosome 17, the position of MYBBP1A was further mapped by radiation hybrid analysis and was found to lie between markers D17S1828 and D17S938. A P1 artificial chromosome clone containing the 5' region of MYBBP1A was isolated and indicates a physical linkage between MYBBP1A and the 15-lipoxygenase gene (ALOX15). A novel, polymorphic (CA)(25) dinucleotide repeat was also isolated from this PAC and may serve as a useful marker for MYBBP1A and this region of chromosome 17.

Alleles↗
PubMed1985

Human genes involved in cholesterol metabolism: chromosomal mapping of the loci for the low density lipoprotein receptor and 3-hydroxy-3-methylglutaryl-coenzyme A reductase with cDNA probes.

Cellular cholesterol metabolism is regulated primarily through the coordinate expression of two proteins, the low density lipoprotein (LDL) receptor and 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase (EC 1.1.1.34). We have used cDNA probes for the human genes encoding these proteins to determine the precise chromosomal location of the two loci. By in situ hybridization we have regionally mapped the LDL receptor gene, LDLR, to the short arm of chromosome 19 in bands p13.1-p13.3. This result concurs with and extends a previous study in which LDLR was mapped to chromosome 19 by screening somatic cell hybrids with a species-specific monoclonal antibody. We have assigned the HMG-CoA reductase gene, HMGCR, to chromosome 5 by Southern blotting of DNA from a somatic cell hybrid panel and to bands 5q13.3-q14 by in situ hybridizations of the cDNA probe to human metaphase cells with normal and rearranged chromosomes.

Cholesterol↗
PubMed1989

Level of expression and chromosome mapping of the mouse cholecystokinin gene: implications for murine models of genetic obesity.

Cholecystokinin (CCK) is a neuropeptide which is present in brain and intestine and which stimulates gall bladder contraction and pancreatic secretion. Additional studies have demonstrated an appetite-suppressing effect of CCK in vivo. These data have aroused speculation that the physiology of this hormone could be relevant in the pathogenesis of the mouse obesity mutations ob on chromosome 6 and db on chromosome 4. In order to determine whether abnormalities of this hormone could be the primary defect in these obesity mutations, we have used three separate approaches to map the mouse Cck gene to distal chromosome 9, where it is part of a syntenic group between mouse chromosome 9 and human chromosome 3. These data therefore exclude cholecystokinin as the etiologic factor in the pathogenesis of any of the known mouse obesity syndromes. In order to exclude the possibility that there are differences in mutant animals in the level of CCK RNA, we have used an S1 nuclease protection assay as well as a novel radioimmunoassay that detects the CCK precursor, to show that there are no gross differences in CCK mRNA or protein precursor levels between ob/ob and wild-type animals.

Alleles↗
PubMed1995

beta-1,4-N-Acetylgalactosaminyltransferase involved in ganglioside synthesis: cDNA sequence, expression, and chromosome mapping of the mouse gene.

beta-1,4-N-Acetylgalactosaminyltransferase (EC 2.4.1.92; GalNAc-T) is a glycosyltransferase involved in the synthesis of gangliosides GM2 and GD2 as well as glycolipid GA2. We have isolated and sequenced the mouse Gal-NAc-T cDNA, studied GalNAc-T mRNA expression in adult tissues and in embryos, and determined the chromosomal location of the GalNAc-T gene, Ggm2. In comparison with the human cDNA, the mouse sequence was 83 and 87% identical at the nucleic acid and amino acid levels, respectively. The GalNAc-T transcript was most abundantly expressed in brain, liver, lung, spleen, and testis among the eight adult tissues examined. Relatively high levels of expression were seen early in mouse development (7-day embryos) compared to later times (11, 15, and 17 days). The Ggm2 gene was mapped to a distal position on mouse chromosome 10 that is homologous to a portion of human chromosome 12.

Amino Acid Sequence↗
PubMed1997

Molecular cloning and chromosome mapping of rat phospholipase D genes, Pld1a, Pld1b and Pld2.

We have previously obtained three partial rat phospholipase D (PLD) cDNA fragments by a reverse transcriptase-polymerase chain reaction (RT-PCR) method using degenerate primers based on two conserved amino acid sequences in PLDs of human and yeast. The entire coding regions of these genes were isolated and sequenced. The longest clone, Pld1a encodes a 1075 amino acid (aa) protein that was highly similar (89% identity) to human PLD1a, especially in four conserved regions present in other PLDs. The nucleotide sequence of the second clone was identical to that of Pld1a except that the clone lacked 114 nucleotides corresponding to 38 aa in the middle. A shorter alternatively spliced form of human PLD1 (PLD1b) lacking the corresponding 38 aa was also identified. Therefore, the second clone (Pld1b) was considered to correspond to the rat counterpart of human PLD1b. The third clone, Pld2 encoding 933 aa was smaller than that of Pld1 and its aa identity to rat Pld1 was 56%. However, it contains four conserved regions and aa sequences of these regions are homologous to those of rat Pld1 and human PLD1. Its entire aa sequence was very similar (96% identity) to the recently cloned mouse PLD, Pld2. Chromosome locations of the Pld1a, Pld1b and Pld2 genes were determined in the rat and mouse by fluorescent in situ hybridization. As expected, both Pld1a and Pld1b clones were hybridized to the same chromosome regions. The Pld1 and Pld2 genes were localized to rat chromosome 2q23.3-->q24 proximal end and the proximal region of mouse Chromosome 3B, and rat chromosome 10q23.3-->q24 proximal end and mouse Chromosome 11B3, respectively. They were mapped in regions where conserved linkage homology has been identified between the two species.

Amino Acid Sequence↗
PubMed1996

Molecular cloning, chromosomal mapping, and characterization of the human cardiac-specific homeobox gene hCsx.

BACKGROUND: Csx/Nkx2.5, a murine nonclustered homeobox gene expressed primarily in the heart, has significant sequence similarity to the Drosophila tinman gene. Tinman is essential for heart and gut formation in Drosophila. Targeted mutation in the mouse gene, Csx/Nkx2.5, arrests cardiac development during early embryonic stages, suggesting an evolutionary conservation in cardiogenesis. MATERIALS AND METHODS: We have isolated and characterized a human homolog, hCsx, from an adult cardiac cDNA library. Northern blotting and ribonuclease protection was used to define the pattern of expression during normal development and in disease states. Chromosomal localization of the gene was determined by somatic cell hybrid analysis and fluorescent in situ hybridization. RESULTS: The predicted amino acid sequence of hCsx has 87% overall homology to the murine gene with 100% identity in the homeodomain. The homeodomain sequence of hCsx is 95% identical to its Xenopus homolog, and 65% to tinman. hCsx mRNA was detected exclusively in the heart. hCsx transcript was detected at 12 weeks in human embryonic heart, the earliest time point examined, and was up-regulated 5-fold between 12 and 19 weeks. There was no significant alteration of hCsx message level in the myocardium of 14 patients with end stage heart failure compared to a normal control. The human gene mapped to the distal portion of chromosome 5, the 5q34-q35 region. This defines a new synteny region between human chromosome 5q and the t-locus of mouse chromosome 17, where the mouse Csx gene is located. CONCLUSIONS: hCsx, the human homolog of Drosophila tinman, is expressed in heart in a tissue restricted manner. Distal 5q trisomies produce several phenotypic abnormalities, including a high incidence of congenital heart disease. Isolation of the hCsx gene will allow further studies of mutations in this gene and their potential associations with some forms of congenital heart disease in humans.

Amino Acid Sequence↗
PubMed2005

Chromosomal mapping of quantitative trait loci controlling elastin content in rat aorta.

Extracellular matrix molecules such as elastin and collagens provide mechanical support to the vessel wall. In addition to its structural role, elastin is a regulator that maintains homeostasis through biologic signaling. Genetically determined minor modifications in elastin and collagen in the aorta could influence the onset and evolution of arterial pathology, such as hypertension and its complications. We previously demonstrated that the inbred Brown Norway (BN) rat shows an aortic elastin deficit in both abdominal and thoracic segments, partly because of a decrease in tropoelastin synthesis when compared with the LOU rat, that elastin gene polymorphisms in these strains do not significantly account for. After a genome-wide search for quantitative trait loci (QTL) influencing the aortic elastin, collagen, and cell protein contents in an F2 population derived from BN and LOU rats, we identified on chromosomes 2 and 14, 3 QTL specifically controlling elastin levels, and a further highly significant QTL on chromosome 17 linked to the level of cell proteins. We also mapped 3 highly significant QTL linked to body weight (on chromosomes 1 and 3) and heart weight (on chromosome 1) in the cross. This study demonstrates the polygenic control of the content of key components of the arterial wall. Such information represents a first step in understanding possible mechanisms involved in dysregulation of these parameters in arterial pathology.

Animals↗
PubMed1998

Murine protein kinase CK2 alpha': cDNA and genomic cloning and chromosomal mapping.

Protein kinase CK2 (casein kinase II) is a heterotetrameric enzyme implicated in many essential regulatory pathways in cells. We have determined the sequence of the murine CK2 alpha' cDNA that encodes a 350-amino-acid protein that would have 99 and 98% homology with the human and chicken proteins, respectively, and is also highly homologous to murine CK2 alpha. To clarify the sequence of the 5' end of the cDNA and to elucidate the structure and regulation of the gene, we obtained a bacterial artificial chromosome clone that contains the 35-kb CK2 alpha' gene. The gene consists of 12 small exons; the 5' end, including the first exon and intron, is extremely GC rich and contains a CpG island. The putative promoter contains potential binding sites for a variety of transcriptional factors but appears to lack CCAAT- or TATA-like elements. A polymorphic dinucleotide repeat in the fifth intron allowed us to map the CK2 alpha' gene to murine Chromosome 8.

Amino Acid Sequence↗
PubMed1998

Chromosomal mapping, tissue distribution and cDNA sequence of four-and-a-half LIM domain protein 1 (FHL1).

We have isolated and sequenced a human heart cDNA clone encoding a novel LIM-only protein. This full-length cDNA clone has a predicted open reading frame (ORF) encoding 280 amino acids. The ORF of this cDNA codes for a LIM-only protein that possesses four repeats of LIM domain and an extra zinc finger and this putative protein is named four-and-a-half LIM domain protein 1 (FHL1). FHL1 is unique when compared with other LIM-only proteins because it possesses an odd number of zinc fingers. When the FHL1 cDNA probe was used to hybridize with poly-(A) RNA of various human tissues, a very strong signal was detected in skeletal muscle, a moderate one in the heart; only weak signals were associated with the placenta, ovary, prostate, testis, small intestine, colon and spleen, and virtually no signal could be detected in brain, lung, liver, kidney, pancreas, thymus and peripheral blood leukocytes. The FHL1 gene was located to human chromosome at Xq27.2 by somatic cell hybrid mapping, fluorescent in situ hybridization (FISH) and radiation hybrid mapping.

Amino Acid Sequence↗
PubMed1995

Chromosomal mapping of the psychomotor stimulant effects of cocaine in BXD recombinant inbred mice.

To elucidate genes associated with cocaine's locomotor stimulant effects, we used recombinant inbred-quantitative trait loci (RI-QTL) analyses to identify chromosomal loci associated with locomotor activity before (baseline) and after cocaine treatment. RI-QTL analyses seek to identify associations between a quantitative measure of a phenotype and one or more previously mapped marker loci across a panel of RI strains. In the present study, 11 BXD RI strains were used to identify several putative QTLs for each phenotype. Both baseline locomotor activity and cocaine's locomotor stimulant effects are polygenic, with both unique and overlapping genetic influences. The largest associations for baseline activity were observed on chromosomes 5 and 9 and the largest associations for cocaine's psychomotor stimulant effects on chromosomes 3 and 17.

Animals↗
PubMed1994

Chromosomal mapping, isolation, and characterization of the mouse xanthine dehydrogenase gene.

Xanthine dehydrogenase (XD) is a key enzyme in the catabolism of purines. A recently isolated XD cDNA clone (Terao et al., Biochem. J. 283, 863-870, 1992) was used to analyze the genomic structure and chromosomal location of this gene. XD was found to be a single-copy gene approximately 70 kb long with 36 exons containing the transcribed sequence. The length of the mouse XD gene was much longer and the structure more complex than those of the Drosophila and Calliphora homologs. The locus encoding the XD gene (designated Xd) was mapped to the distal part of mouse chromosome 17 by haplotype analysis of 114 interspecific backcross mice. Although Xd inactivation may be responsible for xanthinuria, a rare human genetic disease, this genetic locus is not a candidate for any previously described mouse mutation. The transcription start site was defined by primer extension and RNase mapping analysis, using liver mRNA. No other transcription start sites were identified in the liver and a variety of other organs after treatment with an interferon inducer. Transient transfection analysis in NIH3T3, tEnd, and COS cells with an appropriate reporter gene demonstrated that a functional promoter is located within the first 268 bp preceding the transcriptional initiation site.

Amino Acid Sequence↗
PubMed1987

Phosphoribosylpyrophosphate synthetase of Bacillus subtilis. Cloning, characterization and chromosomal mapping of the prs gene.

The gene (prs) encoding phosphoribosylpyrophosphate (PRPP) synthetase has been cloned from a library of Bacillus subtilis DNA by complementation of an Escherichia coli prs mutation. Flanking DNA sequences were pruned away by restriction endonuclease and exonuclease BAL 31 digestions, resulting in a DNA fragment of approx. 1.8 kb complementing the E. coli prs mutation. Minicell experiments revealed that this DNA fragment coded for a polypeptide, shown to be the PRPP synthetase subunit, with an Mr of approx. 40,000. B. subtilis strains harbouring the prs gene in a multicopy plasmid contained up to nine-fold increased PRPP synthetase activity. The prs gene was cloned in an integration vector and the resulting hybrid plasmid inserted into the B. subtilis chromosome by homologous recombination. The integration site was mapped by transduction and the gene order established as purA-guaA-prs-cysA.

Bacillus subtilis↗