Refined sublocalization of the human gene encoding the beta subunit of the S100 protein (S100B) and confirmation of a subtle t(9;21) translocation using in situ hybridization

The gene which encodes the beta subunit of the S100 protein was mapped to 21q22.2----q22.3 by in situ hybridization. Concurrently, a subtle translocation involving this region of chromosome 21 and 9q34 was confirmed.     

The human calbindin D28k (CALB1) and calretinin (CALB2) genes are located at 8q21.3----q22.1 and 16q22----q23, respectively, suggesting a common duplication with the carbonic anhydrase isozyme loci

The genes encoding calbindin D28k (CALB1) and calretinin (CALB2), two closely related calcium-binding proteins, were mapped by in situ hybridization to the 8q21.3----q22.1 and 16q22----q23 regions of the human genome, respectively. These localizations match the chromosomal regions where the carbonic anhydrase isozyme gene cluster (CA1, CA2, CA3) and the related gene CA7 have been described, respectively. This suggests a common duplication o the calbindin/calretinin and the carbonic anhydrase ancestral genes.     

Effect of lysine to alanine mutations on the phosphate activation and BPTES inhibition of glutaminase

The GLS1 gene encodes a mitochondrial glutaminase that is highly expressed in brain, kidney, small intestine and many transformed cells. Recent studies have identified multiple lysine residues in glutaminase that are sites of N-acetylation. Interestingly, these sites are located within either a loop segment that regulates access of glutamine to the active site or the dimer:dimer interface that participates in the phosphate-dependent oligomerization and activation of the enzyme. These two segments also contain the binding sites for bis-2[5-phenylacetamido-1,2,4-thiadiazol-2-yl]ethylsulfide (BPTES), a highly specific and potent uncompetitive inhibitor of this glutaminase. BPTES is also the lead compound for development of novel cancer chemotherapeutic agents. To provide a preliminary assessment of the potential effects of N-acetylation, the corresponding lysine to alanine mutations were constructed in the hGAC_Δ1 plasmid. The wild type and mutated proteins were purified by Ni⁺-affinity chromatography and their phosphate activation and BPTES inhibition profiles were analyzed. Two of the alanine substitutions in the loop segment (K₃₁₁A and K₃₂₈A) and the one in the dimer:dimer interface (K₃₉₆A) form enzymes that require greater concentrations of phosphate to produce half-maximal activation and exhibit greater sensitivity to BPTES inhibition. By contrast, the K₃₂₀A mutation results in a glutaminase that exhibits near maximal activity in the absence of phosphate and is not inhibited by BPTES. Thus, lysine N-acetylation may contribute to the acute regulation of glutaminase activity in various tissues and alter the efficacy of BPTES-type inhibitors.     

The human tyrosine kinase gene (FER) maps to chromosome 5 and is deleted in myeloid leukemias with a del(5q)

A novel member of the SRC tyrosine kinase gene family was recently isolated and characterized (Hao et al., 1989). This FES/FPS-related gene, named FER, lacks the transmembrane and extracellular domains which characterize tyrosine kinases with receptor function. Expression of FER in a wide range of cell types indicates a general role in intracellular signalling or differentiation processes. We have now mapped FER to chromosome 5q14----q23 using in situ hybridization techniques and suggest a more precise location within bands 5q21----q22. This region lies adjacent to a complex domain of growth factors and receptors, many involved in regulation of haematopoiesis. FER maps within a critical segment frequently deleted from chromosome 5 in patients with acute myeloid leukemia or myelodysplastic syndromes and was shown to be deleted in two such patients. It also maps close to the familial polyposis coli locus at 5q22.     

Mapping of the human type II collagen gene (COL2A1) proximal to fra(12) (q13.1) by nonisotopic in situ hybridization

The human type II collagen gene (COL2A1) was mapped to chromosome 12 immediately proximal to fra(12)(q13.1) by the technique of nonisotopic (biotinylated) in situ hybridization. Thus, the COL2A1 gene was confirmed to be at the subband 12q13.11----q13.12, in agreement with previous reports. These results are not in agreement with the localization (12q14.3) cited in Ropers and Craig (1989).     

Assignment of the fucosidase pseudogene FUCA1P to chromosome region 2q31----q32

FUCA1P is a pseudogene of the structural fucosidase gene FUCA1. The former has been mapped to human chromosome 2, whereas the latter has been localized to chromosome 1p34----p36. We have further localized FUCA1P to chromosomal band 2q31----q32 by fluorescent in situ hybridization and digital imaging microscopy. This localization was confirmed by linkage analysis between FUCA1P and the COL3A1 gene in 2q24----q32 which gave maximal lod scores of 4.03 at 3% recombination.     

Physical and cDNA mapping in the DBH region of human chromosome 9q34

Chromosome 9q34 has been extensively studied and mapped due to the presence of known disease genes, principally tuberous sclerosis 1 (TSC1), in this region. During the course of our mapping of this region we constructed a 555-kb contig beginning approximately 50 kb proximal to the dopamine-beta-hydroxylase (DBH) gene and extending, with one small deletion, distal to the D9S114 marker. The contig consists of 11 P1 clones, four PAC clones, one BAC clone and six cosmid clones and contains 27 new nonpolymorphic STSs. We have found the region to be unstable in P1, PAC and BAC cloning vehicles and have identified several deleted genomic clones. In addition, we have isolated and mapped the 3' portions of three putative genes located within or immediately distal to the DBH gene, including one large gene that runs on the opposite strand to DBH and utilizes portions of two DBH exons. The genomic clones of the contig, cDNAs and new STSs will be useful reagents for the further study and mapping of this region.     

Assignment of the human myeloperoxidase gene (MPO) to bands q21.3----q23 of chromosome 17

Using a human myeloperoxidase cDNA, we have mapped the human myeloperoxidase gene to chromosome 17 at q21.3----q23 by in situ hybridization to metaphase chromosomes from human lymphocyte preparations.     

Ontogeny of rdh9 (Crad3) expression: ablation causes changes in retinoid and steroid metabolizing enzymes, but RXR and androgen signaling seem normal

Crad3 (cis-retinol/androgen dehydrogenase 3), a short-chain dehydrogenase/reductase, converts 9-cis-retinol into 9-cis-retinal and 3alpha-androstanediol into dihydrotestosterone. Crad3 may serve in biosynthesis of 9-cis-retinoic acid, a putative RXR ligand, and/or regeneration of potent androgens. RT-PCR showed that expression of the gene that encodes Crad3, rdh9, begins in liver by e11.5, and in kidney, testis, brain and intestine during e15.5-e16.5. In situ hybridization showed rdh9 expression in embryonic liver, ganglia, small intestine, lung, skin and vertebral cartilage. In adult, in situ hybridization revealed rdh9 expression intensely in hepatocytes, weakly in kidney glomerulus, and intensely in collecting tubules. In intestine, undifferentiated epithelia had greater expression than differentiated epithelia at the distal villus end. Testes expressed rdh9 in spermatogonia, and weakly in Leydig cells. Adult brain expressed rdh9 in the dentate gyrus and CA regions of the hippocampus, the cerebellum Purkinje cells, and the glomerular and mitral cell layers of the olfactory bulb. Rdh9-null mice, backcrossed against C57BL/6J mice, were born in Mendelian frequency, were healthy and fertile, and had normal tissue retinoid and serum dihydrotestosterone levels. Expression of rdh1, a gene that encodes an efficient retinol dehydrogenase, decreased 3- to 8-fold in rdh9-null mice, depending on dietary vitamin A. Microarray analysis and quantitative PCR revealed 2- to 4-fold increases in mRNA of enzymes that catalyze xenobiotic and steroid metabolism, including Cyp2, Cyp3, 11beta-hydroxysteroid dehydrogenase type 2, and 17beta-hydroxsteroid dehydrogenases types 4 and 5. These data indicate widespread Crad3 function(s) in steroid and/or retinoid metabolism starting mid embryogenesis.     

The gene coding for proteins HC and HI-30 of inter-alpha-trypsin inhibitor maps to 9q22.3----q33

Proteins HC and HI-30 of inter-alpha-trypsin inhibitor light chain are two plasma proteins. They are encoded by the same monocistronic mRNA. Their function is probably related to the regulation of immunologic and/or inflammatory responses. Using a genomic DNA probe and a panel of somatic cell hybrids we have mapped the gene coding for the proteins to chromosome 9. In situ hybridization experiments refined the assignment to the region 9q22.3----q33.     

The Visual Assignment of Genes by Fiber-Fish: BTF3 Protein Homologue Gene (BTF3) and a Novel Pseudogene of Human RNA Helicase A (DDX9P) on 13q22

Chromosome 13 is one of the poorly mapped human chromosomes. As an example, only two cloned genes have been assigned to bands 13q22–q31. Our characterization of the critical region for the variant form of late infantile neuronal ceroid lipofuscinosis (vLINCL, locus definition CLN5) disease region on 13q22 resulted in the identification of the sequences encoding the BTF3 protein homologue gene (HGMW-approved symbol BTF3) and a novel pseudogene for RNA Helicase A (HGMW-approved symbol DDX9P). Precise visual assignment to the physical clones covering this region and the positional relationships of these genes were achieved by the use of tyramine enhancement of Fiber-FISH hybridization signals, demonstrating the power of this technique in efficient positioning of coding regions on the physical maps.     

Assignment of human erythroid delta-aminolevulinate synthase (ALAS2) to a distal subregion of band Xp11.21 by PCR analysis of somatic cell hybrids containing X; autosome translocations.

The erythroid-specific (ALAS2) and housekeeping (ALAS1) genes encoding delta-aminolevulinate synthase have recently been mapped to chromosomes Xp21.1----q21 and 3p21, respectively. The erythroid-specific gene is a candidate for mutations resulting in X-linked sideroblastic anemia. Analysis of DNA from hybrid clones containing translocations in the region Xp11.21----Xq21.3 permitted the finer localization of the ALAS2 gene with respect to other loci and breakpoints within this region. These studies localized the ALAS2 gene to the distal subregion of Xp11.21 in Interval 5 indicating the following gene order: Xpter-OATL2-[L62-3A, Xp11.21; A62-1A-4b, Xp11.21]-(ALAS2, DXS323)-[B13-3, Xp11.21; C9-5, Xp11.21]-(DXS14, DXS429)-DXS422-(DXZ1, Xcen). Thus, the reported linkage of acquired sideroblastic anemia and sideroblastic anemia with ataxia to Xq13 presumably results from genes other than ALAS2.     

Mapping of the MYC gene to band 8q24.12----q24.13 by R-banding and distal to fra(8)(q24.11), FRA8E, by fluorescence in situ hybridization

The MYC gene was mapped to R-banded human prometaphase chromosomes and to chromosomes expressing fra(8)(q24.11) by fluorescence in situ hybridization. By high-resolution banding analysis, the fluorescent signals were localized to R-positive band q24.12----q24.13 of the long arm of chromosome 8. Furthermore, the signals were localized near the middle part, q24.12----q24.13, of the distal portion of fra(8)(q24.11) expression. Thus, the precise localization of MYC was to the subband 8q24.12----q24.13.     

Human platelet factor 4 gene is mapped to 4q12----q21

The gene for human platelet factor 4 has been mapped to the q12----q21 region of chromosome 4 by in situ hybridization. Hybridization of the same probe to leukemic cells carrying a t(4;11)(q21;q23) showed that the human platelet factor 4 gene is proximal to the breakpoint on chromosome 4.     

Chromosome localization of the human renin gene (REN) by in situ hybridization

Previous studies by Southern blot analysis of human X mouse somatic cell hybrids localized the renin gene to region p21----qter of human chromosome 1. Using a DNA insert encoding exons 2-5, the renin gene was mapped to human chromosome bands 1q25----q32 by in situ hybridization. The sublocalization of the renin gene will facilitate subsequent detailed linkage analysis of human chromosome 1.     

Physical mapping of two loci (D9S5 and D9S15) tightly linked to Friedreich ataxia locus (FRDA) and identification of nearby CpG islands by pulse-field gel electrophoresis

The Friedreich's ataxia locus (FRDA) has recently been mapped to 9q13-q21 by tight linkage to D9S15 and D9S5 loci. The present lack of recombination between these loci precludes further genetic mapping and suggests that the distances involved are in the megabase range. We have established a 1-Mb map around loci D9S15 (defined by probe MCT112) and D9S5 (defined by probe DR47) and found that they are at most 260 apart. Six rare cutting site clusters were found in a 450-kb segment containing both loci. Three clusters were completely unmethylated in two cell lines tested and might correspond to CpG islands flanking transcribed sequences. Cosmid mapping of a 52-kb region around D9S5 and pulse-field gel electrophoresis analysis showed the presence of three other CpG clusters that were partially or completely methylated. Two of them were present in the cosmid clones available and were associated with sequences conserved in other vertebrate species. The CpG islands and conserved sequences presented here can be used to search for genes defective in Friedreich's ataxia.     

Chromosomal localization of the human gene for annexin V (placental anticoagulant protein I) to 4q26----q28.

Annexin V is a member of a new family of calcium-dependent phospholipid-binding proteins. It has been previously isolated as placental anticoagulant protein I, inhibitor of blood coagulation, vascular anticoagulant-alpha, endonexin II, lipocortin V, placental protein 4, and anchorin CII. The human gene encoding annexin V (ANX5) was localized to 4q26----q28 by in situ hybridization with a cDNA probe and polymerase chain-reaction (PCR) analysis of a human x hamster hybrid cell panel. The regional localization to 4q26----q28 was supported by Southern-blot analysis of a human cell line with a deletion in 4q23----q27. This localization overlaps but differs slightly from the previous assignment of ANX5 to 4q28----q32. Digestion with PvuII and TaqI identified polymorphisms at the ANX5 locus; the PvuII polymorphism could also be detected by PCR analysis.     

Assignment of the human dihydrofolate reductase gene to the q11----q22 region of chromosome 5.

Cells from a dihydrofolate reductase-deficient Chinese hamster ovary cell line were hybridized to human fetal skin fibroblast cells. Nineteen dihydrofolate reductase-positive hybrid clones were isolated and characterized. Cytogenetic and biochemical analyses of these clones have shown that the human dihydrofolate reductase (DHFR) gene is located on chromosome 5. Three of these hybrid cell lines contained different terminal deletions of chromosome 5. An analysis of the breakpoints of these deletions has demonstrated that the DHFR gene resides in the q11----q22 region.