Partial Genomic Clone Research Articles

Uroguanylin and guanylin: Distinct but overlapping patterns of messenger RNA expression in mouse intestine

BACKGROUND & AIMS: Uroguanylin and guanylin, endogenous ligands of the guanylate cyclase C receptor, are presumed to mediate fluid and electrolyte secretion in the intestine. The aim of this study was to characterize the expression patterns of uroguanylin and guanylin messenger RNA (mRNA) in the mouse intestine. METHODS: A mouse uroguanylin complementary DNA was amplified from a partial genomic clone, and Northern analyses and in situ hybridization were performed to localize guanylin and uroguanylin mRNA along the duodenal-colonic and crypt-villus axes. RESULTS: Uroguanylin mRNA was expressed throughout the mouse intestine and also in the kidney. Signal intensity was greatest in the small intestine for uroguanylin and in the distal small intestine and colon for guanylin. In situ hybridization showed uroguanylin mRNA localized predominantly in intestinal villi and the corticomedullary junction of the kidney, whereas guanylin mRNA was localized in both crypts and villi in the small intestine and to superficial epithelial cells in the colon. CONCLUSIONS: Mouse uroguanylin mRNA expression is discrete from guanylin expression in the intestine. The patterns of distribution in the intestine and the known pH optima of these ligands suggest a complementary role for these secretagogues. (Gastroenterology 1997 Sep;113(3):1000-6)

Chromosomal Localization of the Human Urothelial “Tetraspan” Gene, UPK1B, to 3q13.3–q21 and Detection of aTaqI Polymorphism

The TI1/UPK1b gene codes for a protein of the “tetraspan” family and is expressed as a differentiation product of the mammalian urothelium. A partial genomic clone of the human homologue of the TI1/UPK1b gene was isolated and used as probe to localize the human gene to chromosome 3q13.3–q21 byin situhybridization. Using the same probe, aTaqI restriction fragment length polymorphism, with 29% heterozygosity, was identified by Southern analysis.

Identification of a delta-TIP cDNA clone and determination of related A and D genome subfamilies in Gossypium species.

Tonoplast intrinsic proteins (TIPs) have been implicated in the process of cell elongation, such as occurs in the developing cotton fiber. We have isolated a cDNA clone (997 bp in length) from a cotton (Gossypium hirsutum L.) library which putatively encodes a protein of 248 residues (Mr 25079) with 85% identity to Arabidopsis delta-TIP. The derived amino acid sequence included two conserved sequences associated with major intrinsic proteins (SGxHxNPA at residues 78 to 85, NPA residues at 197 to 199) and a cysteine residue at 116 which is reported to bind mercury in Arabidopsis delta-TIP. The polymerase chain reaction was used to generate partial genomic clones of the cotton delta-TIP. In comparison to other genomic TIP sequences, the number (two) and position of the introns were conserved in cotton. Comparing the TIP sequences from cotton revealed two subfamilies, which were consistently distinguished by a Tsp45I restriction site polymorphism. This polymorphism was used to demonstrate that TIP subfamilies were specific to either the A or D genomes of Gossypium. When delta-TIP DNA fragments were amplified from cDNA of fiber 14 days after anthesis, the A and D were found, indicating the presence of delta-TIP transcripts in these elongating cells.

The mouse poly(C)-binding protein exists in multiple isoforms and interacts with several RNA-binding proteins.

The murine poly(C)-binding protein (mCBP) was previously shown to belong to the group of K-homology (KH) proteins by virtue of its homology to hnRNP-K. We have isolated cDNA-splice variants of mCBP which differ by two variable regions of 93 bp and/or 39 +/- 3 bp respectively. Both variable regions are located between the second and third KH-domain of mCBP. The characterization of a partial genomic clone enabled us to propose a model for the generation of the second variable region by the use of a putative alternative splice signal. The mCBP mRNA is expressed ubiquitously and the protein is found predominantly in the nucleus with the exception of the nucleoli. We have identified five proteins which interact with mCBP in the yeast two hybrid system: mouse y-box protein 1 (msy-1), y-box-binding protein, hnRNP-L, filamin and splicing factor 9G8. The interaction between mCBP and splicing factor 9G8 was confirmed in vivo. These results suggest a function of mCBP in RNA metabolism.

Cloning and chromosomal localization of a novel gene-encoding a human β2-integrin α subunit

We isolated a partial genomic clone encoding ITGAD, a novel β 2-integrin α subunit. The ITGAD gene is highly homologous to the three previously known α subunit-encoding genes, that compose the β 2 integrin family, in deduced amino acid sequence, intron/exon structure and mapping location (chromosome 16p11).

Chromosomal Mapping of the Human M6 Genes

M6 is a neuronal membrane glycoprotein that may have an important role in neural development. This molecule was initially defined by a monoclonal antibody that affected the survival of cultured cerebellar neurons and the outgrowth of neurites. The nature of the antigen was discovered by expression cDNA cloning using this monoclonal antibody. Two distinct murine M6 cDNAs (designated M6a and M6b) whose deduced amino acid sequences were remarkably similar to that of the myelin proteolipid protein were previously isolated. We have isolated partial human cDNA and genomic clones encoding M6a and M6b and have characterized them by restriction mapping, Southern hybridization with cDNA probes, and sequence analysis. We have localized these genes within the human genome by FISH (fluorescencein situhybridization). The human M6a gene is located at 4q34, and the M6b gene is located at Xp22.2. A number of human neurological disorders have been mapped to the Xp22 region, including Aicardi syndrome (MIM 304050), Rett syndrome (MIM 312750), X-linked Charcot–Marie–Tooth neuropathy (MIM 302801), and X-linked mental retardation syndromes (MRX1, MIM 309530). This raises the possibility that a defect in the M6b gene is responsible for one of these neurological disorders.

Identification and characterization of a new major histocompatibility complex class I gene in carp (Cyprinus carpio L.)

In this study we report the finding of three representatives of a new group of major histocompatibility complex class I sequences in carp: Cyca-12 (Cyca-UA1*01), a full-length cDNA; Cyca-SP1 (Cyca-UAW1), a polymerase chain reaction (PCR) fragment from cDNA; and Cyca-G11 (Cyca-UA1*02), a partial genomic clone. Comparison of the amino acid sequences of Cyca-12, Cyca-SP1, and Cyca-G11 with classical and non-classical class I sequences from other species shows considerable conservation in regions that have been shown to be involved in maintaining the structure and function of class I molecules. The genomic organization of Cyca-12 has been elucidated by analysis of a partial genomic clone (Cyca-G11, in combination with PCR amplifications on genomic DNA of a homozygous individual. Although the genomic organization is similar to that found in class I genes from other species, the 3' untranslated region contains an intron which is unprecedented in class I genes, and intron 2 is exceptionally large (+/-14 kilobases). Southern blot analysis indicates the presence of multiple related sequences. In phylogenetic analyses, the Cyca-UA sequences cluster with class I genes from zebrafish and Atlantic salmon, indicating that the ancestral gene arose before the salmonid/cyprinid split, approximately 120-150 million years ago. The previously reported class I Cyca-Z genes from carp and Caau-Z genes from goldfish cluster as a completely separate lineage. A polyclonal antiserum (anti-Cyca12) was raised against a recombinant fusion protein containing most of the extracellular domains of Cyca-12. The antibodies showed substantial reactivity to the recombinant protein and an Mr 45000 protein in membrane lysates of spleen and muscle, as well as to determinants present on leucocytes in fluorescence-activated cell sorter analyses. Erythrocytes and thrombocytes were found to be negative.

Mucopolysaccharidosis IVA: Submicroscopic deletion of 16q24.3 and a novel R386C mutation of n-acetylgalactosamine-6-sulfate sulfatase gene in a classical Morquio disease

The N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene, which is responsible for autosomal recessive mucopolysaccharidosis IVA (MPSIVA), has been assigned to the long arm of chromosome 16, subregion 24.3, an area where the adenine phosophoribosyltransferase (APRT) gene and renal dipeptidase (DPEP I) gene are also localized. Molecular genetic studies on a severely affected patient with MPSIVA (Morquio disease), without karyotypic abnormality, revealed a partial submicroscopic deletion of 16q24.3 and a single point mutation on the other allele, with no functional GALNS activity. The patient, his mother, and siblings were hemizygous for GALNS and APRT loci, evidenced by informative RFLP and gene dosage analyses combined with a fluorescence in situ hybridization, utilizing a partial genomic clone of GALNS, but heterozygosity was retained at the DPEP I locus and proximal D16S7. Haplotyping of the family members revealed recombinational events between DPEP I locus and three other polymorphic loci on the paternal chromosome, localizing GALNS gene on the proximal side to DPEP I gene. As estimated from the genetic distance between two flanking markers of proximal D16S7 and distal DPEP I locus, size of the deletion was less than 3Mb. Mother of the boy and two older siblings were asymptomatic, despite this interstitial deletion of the Giemsa-light G band. The remaining paternal allele had no gene rearrangement but GALNS activity was not encoded as Arginine at 386 was replaced with Cysteine (R386C), suggesting this alteration accounts for the severe phenotype. Allelic loss of APRT is frequently observed in cancer tissues, thereby suggesting that the tumor suppressor gene locates near the APRT locus. No family member has evidence of any malignant disease. This study is apparently the first documentation of interstitial deletion of 16q24.3, involving GALNS and APRT genes.

Cloning of a New "Finger" Protein Gene (ZNF173) within the Class I Region of the Human MHC

The human major histocompatability complex contains genes of both immune and nonimmune importance. Recently, several genes encoding novel, non-HLA products have been described in this area. We have performed positional cloning of short fragment cDNA sequences from the class I region of the human MHC using a hybridization selection approach. This report describes isolation of full-length cDNA clones and partial genomic clones that encode a protein that contains two domains rich in cysteine and histidine similar to those characteristic of metal-dependent DNA binding proteins (C3HC4). The predicted protein also contains a domain thought to form a coiled-coil that may promote dimerization. A third feature is a polyglutamic acid region near the carboxyl terminus of the conceptual protein. Because of these properties, we have named this gene product acid finger protein (AFP). Although the biological role of AFP is unknown at present, one potential function is binding of nucleic acids. The gene (ZNF173) is expressed in multiple tissues and is conserved among mammals. In particular, the mouse and human coding regions are highly conserved. In addition to AFP, other related sequences have been localized to the MHC, suggesting that multiple AFP-like genes exist in this area.

Isolation and characterization of an avian A1 adenosine receptor gene and a related cDNA clone

We have isolated the gene for a chick A1 adenosine receptor along with a cDNA that codes for the same adenosine receptor. The cDNA clone was isolated from both adipose tissue and heart cDNA libraries and encodes a 324-amino acid protein with 80% identity with mammalian A1 adenosine receptors. Transient expression of the cDNA in human embryonic kidney (HEK) 293 cells shows that it encodes a protein that binds [3H]CCPA (2-chloro-N6-[cyclopentyl-2,3,4,5-3H]cyclopentyladenosine, a specific agonist radioligand, with a KD of 5.6 +/- 2.4 nM. Cyclic AMP measurements in HEK 293 cells co-transfected with the chick cDNA and a cDNA for a luteinizing hormone/choriogonadotropin receptor shows that A1 adenosine receptor agonists antagonize the cyclic AMP-elevating effect of bovine luteinizing hormone. Two partial genomic clones were isolated. The first contains 5'-untranslated sequence including a putative promoter region which does not contain a TATA box, an intron and the first third of the coding sequence of the A1 adenosine receptor cDNA. The coding sequence of this partial genomic clone terminates at a second intron. The second partial genomic clone contains the rest of the coding sequence and the 3'-untranslated elements in a single exon. Thus the chick A1 adenosine receptor gene contains one intron in the 5'-untranslated region and a minimum of one intron in the coding sequence.

Chromosomal assignment and genomic structure of Il15

Interleukin-15 (IL-15) is a novel cytokine whose effects on T-cell activation and proliferation are similar to those of interleukin-2 (IL-2), presumably because IL-15 utilizes the β and γ chains of the IL-2 receptor. Murine IL-15 cDNA and genomic clones were isolated and characterized. The murine Il15 gene was found to consist of eight exons spanning at least 34 kb and was localized to the central region of mouse chromosome 8 by interspecific backcross analysis. Intron positions in a partial human IL15 genomic clone were identical with positions of corresponding introns in the murine gene. The human IL15 gene was mapped to human chromosome 4q31 by fluorescence in situ hybridization.

A cdc2 homologue and closely related processed retropseudogenes from Norway spruce

The p34cdc2 protein kinase is a key component in the regulation of the eukaryotic cell cycle and has been conserved during evolution. We have isolated cDNA clones corresponding to a cdc2 gene (cdc2Pa) from the conifer Norway spruce, Picea abies (L.) Karst. The deduced amino acid sequence is 85-90% identical to p34cdc2 homologues from other plants, contains eleven subdomains characteristic for the protein kinase family, and three sequence motifs specific for the cdc2 protein kinases. A partial genomic clone of cdc2Pa reveals two introns at positions identical to intron positions in Arabidopsis thaliana cdc2a. A Southern blot analysis shows that cdc2Pa is a single-copy gene belonging to a family of about 10 related genes. Partial genomic sequences of six of the genes in this family (86-92% identical to cdc2Pa) show distinct features of processed retropseudogenes. These lack introns and contain deletions, insertions and/or non-silent point mutations. This result is consistent with the hypothesis that processed retropseudogenes in plants may be common among genes expressed in the apical meristem, that is, in cells which have the potential to take part in the formation of reproductive organs. Although cdc2Pa transcripts were abundant in the epicotyl and thus likely in the apical meristem, we observed no strict coupling of expression to cell division in embryos and seedlings.

Cloning and characterization of a murine macrophage lipoxygenase

We have isolated a murine macrophage cDNA encoding a 12-lipoxygenase, that represents the homolog of the human 15-lipoxygenase. The predicted amino acid sequence of this lipoxygenase is highly similar to the rat 12-lipoxygenase isolated from brain and human 15-lipoxygenase. The recombinant enzyme expressed in Cos-7 cells oxidizes arachidonic acid to 12- and 15-HETE with a profile similar to that obtained from peritoneal macrophages. A polyclonal antibody generated against a putative peptide recognizes a 75 kDa protein in cell extracts from mouse peritoneal macrophages and transfected Cos-7 cells. The lipoxygenase cDNA hybridizes to a 2.5 kb mRNA present in peritoneal macrophages, lung, spleen, heart and liver. RT-PCR analysis indicates that the same lipoxygenase is expressed in mouse reticulocytes. A partial genomic clone for this lipoxygenase has also been characterized. Southern blot analysis of mouse genomic DNA indicates that this is a single copy gene.

Chromosomal location and some structural features of human clathrin light-chain genes (CLTA and CLTB).

Two human clathrin light-chain genes have been defined. The gene (CLTA) encoding the LCa light chain maps to the long arm of chromosome 12 at 12q23-q24 and that encoding the LCb light chain (CLTB) maps to the long arm of chromosome 4 at 4q2-q3. Isolation and characterization of partial genomic clones encoding human LCa and LCb reveal the neuron-specific insertions of the LCa and LCb proteins to be encoded by discrete exons, thus proving that clathrin light chains undergo alternate mRNA splicing to generate tissue-specific protein isoforms. The insertion sequence of LCb is encoded by a single exon and that of LCa by two exons. The first of the two neuron-specific LCa exons is homologous to the corresponding LCb exon. An intronic sequence of the LCb gene with similarity to the second neuron-specific exon of the LCa gene has been identified.

Human Mitochondrial HMG CoA Synthase: Liver cDNA and Partial Genomic Cloning, Chromosome Mapping to 1p12-p13, and Possible Role in Vertebrate Evolution

Mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase (mHS) is the first enzyme of ketogenesis, whereas the cytoplasmic HS isozyme (cHS) mediates an early step in cholesterol synthesis. We here report the sequence of human and mouse liver mHS cDNAs, the sequence of a HS-like cDNA from Caenorhabditis elegans, the structure of a partial human mHS genomic clone, and the mapping of the human mHS gene to chromosome 1p12-p13. The nucleotide sequence of the human mHS cDNA encodes a mature mHS peptide of 471 residues, with a mean amino acid identity of 66.5% with cHS from mammals and chicken. Comparative analysis of all known mHS and cHS protein and DNA sequences shows a high degree of conservation near the N-terminus that decreases progressively toward the C-terminus and suggests that the two isozymes arose from a common ancestor gene 400-900 million years ago. Comparison of the gene structure of mHS and cHS is also consistent with a recent duplication event. We hypothesize that the physiologic result of the HS gene duplication was the appearance of HS within the mitochondria around the time of emergence of early vertebrates, which linked preexisting pathways of beta oxidation and leucine catabolism and created the HMG CoA pathway of ketogenesis, thus providing a lipid-derived energy source for the vertebrate brain.

The legumin gene family: a reconstructed Vicia faba legumin gene encoding a high-molecular-weight subunit is related to type B genes.

Nucleotide sequence information from a partial genomic clone, a cDNA clone, a RACE clone and a PCR fragment was combined to reconstruct the first reported complete gene sequence encoding a large legumin subunit, designated LelB3. The length difference to the well-characterized major legumin subunits is caused by an extended glutamine/glutamic acid-rich region encoded by the C-terminal part of the alpha chain. Amino acid sequence comparisons reveal that gene LelB3 is more closely related to B-type than to A-type legumin genes of Vicia faba. Gene LelB3 is a member of a small gene family as indicated by published (Pich and Schubert, Biol Zbl 112 (1993); 342-350) and limited own data.

Rabbit interleukin-1 receptor antagonist. Cloning, expression, functional characterization, and regulation during intestinal inflammation.

Genomic and cDNA clones for rabbit interleukin-1 receptor antagonist (IL-1ra) were isolate based on homology with the human, mouse, and rat IL-1ra gene. A partial genomic clone, obtained by screening a rabbit genomic library, contained coding sequences for the carboxyl-terminal 108 amino acids of rabbit IL-1ra. Two classes of cDNA for rabbit IL-1ra were obtained using RNA from inflamed rabbit colon tissue. One class of cDNA coded for a secreted form of IL-1ra, whereas the other coded for a putative intracellular form of rabbit IL-1ra. The latter form is similar to that isolated from human epithelial cells. A partially synthetic rabbit IL-1ra gene was constructed and expressed in Escherichia coli. The recombinant rabbit IL-1ra was purified to homogeneity by ion exchange chromatography. Its affinity was similar to that of human IL-1ra for the human and mouse type I IL-1 receptor. From the cDNA clone and the purified recombinant protein, specific probes were developed for measuring levels of rabbit IL-1ra mRNA and protein in normal and inflamed rabbit tissues. Unlike IL-1 alpha and IL-1 beta, IL-1RA mRNA and protein were present at detectable levels in normal rabbit colon. During the development of an experimental formalin-immune complex colitis, rabbit IL-1 alpha showed a dramatic increase in tissue levels, consistent with previous results; IL-1ra also increased 3-4-fold. Treatment of colitis rabbits with corticosteroids significantly suppressed neutrophil infiltration, corticosteroid treatment suppressed IL-1ra but not IL-1 alpha mRNA steady-state levels. Our observations demonstrate that IL-1 and IL-1ra synthesis is differentially regulated in healthy and inflamed intestinal tissue.

A 3.5 kb deletion in the glycophorin C gene accounts for the Gerbich-negative blood group in Melanesians.

The Gerbich-negative blood group types are rare in most populations, but reach appreciable frequencies in certain Melanesian groups in Papua New Guinea. The recent cloning of the human glycophorin C (GPC) gene, that encodes Gerbich (Ge) blood group antigens, has facilitated study of its genetic variants. We have obtained partial genomic clones of a normal GPC gene, for molecular analysis of Ge: -1, -2, -3 types in Melanesians, and have shown that a 3.5 kb deletion in the GPC gene that removes all of exon 3 accounts for at least one Gerbich-negative phenotype in Melanesians. Population distributions of GPC RFLP have shown that the deletion-type GPC is not confined to mainland Papua New Guinea as previously thought, but occurs sporadically in Melanesians from Fiji as well as in Micronesians.

Rat desmin gene structure and expression

The isolation of two partial genomic clones and a near full length cDNA clone encoding the rat intermediate filament protein desmin is reported. Desmin is a differentiation marker for all types of muscle cells. The nucleotide order of the coding region and 0.1 kb of 5′-flanking sequences of the rat desmin gene has been determined. One genomic clone encompasses exons I–III and approx. 12 kb of 5′-flanking sequences, while the other clone contains exons VII–IX and about 12 kb of 3′-flanking sequences. Northern analysis of RNA from different organs reveals that, as expected, desmin is expressed in striated, heart and smooth muscle cells containing tissues; among other tissues, lung displays relatively high expression levels, while desmin mRNA is barely detectable in spleen, kidney and liver. S1 mapping reveals that the same transcription initiation site is used in all desmin mRNA containing tissues.

Recombinant Human Thyroid Stimulating Hormone: Development of a Biotechnology Product for Detection of Metastatic Lesions of Thyroid Carcinoma

We have genetically engineered a cell line, and developed a reproducible process, for the expression and purification of biologically active recombinant human thyroid stimulating hormone (rhTSH).rhTSH was expressed by co-transfecting a human alpha-subunit cDNA with a human beta-subunit partial genomic clone into Chinese Hamster Ovary (CHO) cells. Stable transfectants which expressed high levels of rhTSH were selected, and subsequently cultured on microcarrier beads. The rhTSH-containing media, produced under serum-free conditions, was clarified and purified by a combination of ion exchange, dye and gel filtration chromatographies. Individual step recoveries were greater than 90% with the exception of a very conservative pooling of the final gel filtration step (78% recovery) that resulted in a cumulative yield of 54% for the purification process. Purity of the final bulk material was judged to be > 99% by SDS polyacrylamide gel electrophoresis (SDS-PAGE), reverse phase HPLC, and size exclusion chromatography. Initial characterization of the oligosaccharide composition indicated the presence of partially sialylated bi- and triantenary complex oligosaccharides. Purified rhTSH was active in a thyroid membrane bioactivity assay with a specific activity of 8.2 IU/mg. The in vivo activity of rhTSH in cynomolgus monkeys appeared to be equal to or greater than that reported for bovine TSH (bTSH) in human subjects. The rapid clearance phase half-life of rhTSH was approximately 35 minutes while the post-distribution phase half life was approximately 9.8 hours. Furthermore, the monkeys showed cumulative increases in minimum plasma rhTSH levels when given three daily intramuscular (IM) rhTSH injections; a phenomenon not observed when bTSH had been administered to humans. The rhTSH showed no evidence of toxic or adverse effects when administered at doses up to 7.2 IU/kg and 0.52 IU/kg in rat and monkey, respectively. These are 50X and 4X multiples of the bTSH doses of 0.143 IU/kg (10 IU/70kg) previously administered to humans.