Genomic organization and assignment of the interleukin 7 gene (IL7) to porcine chromosome 4q11-->q13 by FISH and by analysis of radiation hybrid panels

Interleukin 7 (IL7) is a cytokine that has many immunological functions, including regulation of hematopoiesis and peripheral lymphocytes. cDNA and a genomic DNA segment containing the porcine IL7 gene were isolated and sequenced, showing that porcine IL7 consists of 176 amino acids and that its gene spans over about 13 kb of genomic DNA. Porcine IL7 has 85% and 73% homology with human IL7 in terms of the nucleotide and amino acid sequences, respectively. Whereas the murine IL7 gene does not have an exon corresponding to human exon 5 (Lupton et al., 1990), the porcine IL7 gene was found to contain the same exon-intron structure as the human gene. These findings, together with the upstream structure of the cDNA elucidated in the present study, indicate that the relationship between swine and human IL7 is closer than that between mouse and human IL7. The IL7 gene was mapped to swine chromosome 4q11-->q13 by fluorescence in situ hybridization and, using a radiation hybrid panel, was localized between microsatellite markers Sw1336 and Sw1073 on the same chromosome.     

Structure and Polymorphism Analysis of Transforming Growth Factor Beta Receptor 1 (TGFBR1) in Pigs

Many quantitative trait loci (QTL) for growth and reproductive traits have been detected on the porcine chromosome region 1qter (SSC1qter), making it one of the most important genomic regions for pig breeding. SSC1q corresponds to human chromosome 9, on which lies transforming growth factor beta receptor 1 (TGFBR1). We cloned the porcine TGFBR1 cDNA and gene (as a candidate for QTL) and analyzed the gene structure and polymorphism. Porcine TGFBR1 consists of 9 exons and 8 introns. Intron 2 is alternatively spliced at the acceptor site, resulting in two kinds of mRNA, with putative open reading frames of 1500 and 1512 bp in length. The shorter one encodes 499 amino acid residues. The amino acid sequence has 96.2 and 97.2% sequence similarity to those of human and bovine TGFBR1, respectively. The sequence similarity between porcine and murine TGFBR1 is 95.6%. We detected three single-nucleotide substitutions in exons 1, 2, and 7. Those in exons 1 and 7 are nonsynonymous substitutions resulting in Pro8Ser and Ile413Val substitutions, respectively.     

A novel porcine gene,alpha-1-antichymotrypsin 2 (SERPINA3-2): sequence,genomic organization,polymorphism and mapping

A novel porcine gene, alpha-1-antichymotrypsin 2 (SERPINA3-2), a member of the serpin superfamily, was isolated from a porcine genomic library and sequenced. The genomic organization of the approximately 9.0 kb gene was determined on the basis of the porcine liver cDNA of SERPINA3-1 and SERPINA3-2, and comprises five exons and four introns. The coding sequence of SERPINA3-2 shares 86% identity with the paralogue, SERPINA3-1. Porcine SERPINA3-2 was found to be an orthologue of human SERPINA3 (71% identity of the coding sequences) and both genes have a similar genomic organization. Polymorphisms were found in intron 4 of the porcine gene using polymerase chain reaction-restriction fragment length polymorphism. The gene was mapped by linkage analysis and radiation hybrid mapping to the distal end of chromosome 7q, to the gene cluster of the protease inhibitors including PI1 (SERPINA1), PI2, PI3, PI4 (apparently paralogues of SERPINA3), and PO1A and PO1B. SERPINA3-2 is the first porcine serpin gene whose genomic organization has been determined.     

Genomic structure of swine taste receptor family 1 member 3, TAS1R3, and its expression in tissues

Taste receptor family 1 member 3, TAS1R3, is shown to be involved in sweet and umami tastes in mouse, and the nucleotide sequence of the gene has been reported in rat, gorilla, and human. Pigs are frequently used as models for human diseases, and are also considered to be source animals for xenotransplantation to humans due to their anatomical and physiological similarities to humans. Therefore, in the present study, the genomic structure of the swine TAS1R3 gene was determined, and TAS1R3 expression was studied in various swine tissues. The gene was shown to reside on swine chromosome 6q22-->q23, from which three types of mRNAs were generated: 3,752 bp derived from six exons in tongue, 3,704 bp from six exons and 3,630 bp from seven exons in testis. The 6 exons/5 introns were structurally similar to those of humans and mice, but the 7 exons/6 introns structure of TAS1R3 was first observed in swine. High expressions of TAS1R3 were revealed in tongue, kidney, and testis by real-time PCR. The expression profile of the tissues except for kidney was similar to that of mouse. When in situ hybridization using an RNA probe for TAS1R3 was performed on swine tongue and testis tissues, TAS1R3 expressions were revealed in tongue circumvallate papillae, fungiform papillae, mucosal epithelium, follicular B lymphocytes, lymphocytes in submucosal tissues of lingual tonsil, and spermatogenic cells. Using peripheral mature B lymphocytes, the expression of TAS1R3 in B lymphocytes was further confirmed by real-time PCR and sequencing of the real-time PCR product.     

Papillary renal cell carcinoma: analysis of germline mutations in the MET proto-oncogene in a clinic-based population

Approximately 10% of all renal cell carcinomas (RCCs) present a distinctive papillary histology. Familial papillary RCC (PRCC) has been described, but the majority of cases appear to be sporadic. Recently, germline mutations in the MET proto-oncogene on chromosome 7 have been identified in families with hereditary PRCC. We evaluated 59 patients with PRCC for the frequency of MET germline mutations to determine the value of genetic screening of this patient population. Between 1976 and 1997, 165 patients were identified with PRCC by retrospective chart review. Fifty-nine of 133 surviving patients agreed to provide a family history, a blood specimen, and informed consent for genetic research. DNA was isolated from peripheral blood leukocytes. Denaturing high-performance liquid chromatography (DHPLC) followed by genomic sequencing was performed on eight exons of the MET proto-oncogene, including exons 5-7 of the extracellular domain, exon 14, and exons 16-19 of the tyrosine kinase domain. The 59 patients in this study included 49 men and 10 women with a mean age at diagnosis of 61 years. Bilateral and/or multifocal disease was present in 13 cases (22%). No germline mutations were detected in the studied exons of the MET proto-oncogene (exons previously reported to contain deleterious mutations in familial PRCC). No pathological MET proto-oncogene germline mutations were identified in 59 patients with PRCC. The germline mutation rate in this clinic-based population of individuals with PRCC approaches 0% (CI = 0-6.18). MET proto-oncogene germline mutation screening does not appear to be clinically indicated in patients with PRCC without additional evidence for a genetic predisposition (positive family history, unusual age at onset, bilateral disease).     

Genetic and physical mapping, expression analysis and partial sequence of porcine PER1

The porcine PER1 gene was mapped to chromosome 12q1.4-->q1.5 using fluorescence in situ hybridisation. A polymorphic microsatellite marker (S0601) was isolated from a BAC clone shown to contain the PER1 gene. Linkage analysis assigned S0601 distal to ALOX12 on SSC12, providing further evidence for the conservation of synteny between HSA17 and SSC12. RT-PCR analysis demonstrated the expression of PER1 in all 11 tissues tested, consistent with the data from other mammalian species. Part of the PER1 gene was sequenced, homologous to exons 2-14 of the human gene and encoding the N-terminus of porcine PER1. The predicted amino acid sequence of the partial pig PER1 protein shares over 96% identity with its human orthologue.     

Morphine activation of c-fos expression in rat brain

The post-receptor mechanism of opiate action has been studied by examining the activation by morphine of the proto-oncogene c-fos and its encoded nucleoprotein pp55c-fos (FOS) in rat caudate-putamen, which is rich in the mu-type opiate receptor. Following an acute morphine treatment, c-fos mRNA levels in rat caudate-putamen were increased to maximum (420% of control level) at 45 minutes and returned to control levels at 90 minutes. This induction was completely abolished by naloxone, a morphine antagonist. Fos protein, detected by immunocytochemistry, was also increased 3 hours after morphine injection, in the caudate-putamen, but not in the olfactory tubercle, which does not have the mu-type opiate receptor. Upon activation of opiate receptors by morphine, the c-fos gene is activated and Fos protein may act as a signal transducer uniquely involved in the mechanism of opiate addiction at the level of gene regulation.     

Genomic structure and gene order of swine chromosome 7q1.1-->q1.2

To clarify the structure of the porcine genomic region that contains quantitative trait loci (QTL) related to fat, we constructed a bacterial artificial chromosome (BAC) contig of the region from DST to SRPK1 on porcine chromosome 7 and performed low-redundancy 'skim' shotgun sequencing of the clones that composed a minimum tiling path of the contig. This analysis revealed that the gene order from VPS52 to SRPK1 is conserved between human and swine and that comparison with the human sequence identified a rearrangement in the swine genome at the proximal end of VPS52. Analysis of the nucleotide sequences of three BAC clones that included the rearrangement point demonstrated that COL21A1 and DST, which were not present in the corresponding human region, were located adjacent to the rearrangement point. These results provide useful information about the genomic region containing QTL for fat in pigs and help to clarify the structure of the so-called 'extended-class II' region distal to the porcine major histocompatibility complex class II region.     

Angiotensin-II-induced expression of proto-oncogene (c-fos, jun-B and c-jun) mRNA in bovine adrenocortical fasciculata cells (BAC) is mediated by AT-1 receptors.

We have shown previously that angiotensin-II (A-II) controls proto-oncogene (c-fos, jun-B and c-jun) mRNA accumulation in bovine adrenal fasciculata cells (BAC). Since BAC contain both subtypes (AT-1 and AT-2) of the A-II receptor, we have investigated which subtype was involved in the effect of A-II on proto-oncogene mRNA by using a selective antagonist for AT-1 (DUP 753) and for AT-2 (CGP 42112A). DUP 753, but not CGP 42112A, inhibited the stimulatory effect of A-II on proto-oncogene mRNA, with ID50s of 4 x 10(-7) M, 7 x 10(-7) M and 2 x 10(-6) M for c-fos, jun-B and c-jun, respectively. Neither of the two antagonists by themselves had a direct effect on proto-oncogene mRNA. As the A-II AT-1 receptors are coupled to the phospholipase C system in BAC, we have investigated whether the A-II effects on the proto-oncogenes were mediated by protein kinase C (PKC) or by Ca2+ calmodulin. First, activation of PKC by the phorbol ester, PMA, increased the level of three proto-oncogene mRNAs, whereas calcium ionophore had no effect. Second, staurosporine, a specific inhibitor of PKC, reduced the stimulatory action of A-II on proto-oncogene mRNA by 80-90%, whereas trifluoroperazine, an inhibitor of calmodulin, had no significant effect. These results demonstrate that the effects of A-II on proto-oncogene mRNA are mediated by AT1 receptor subtypes, mainly through activation of the PKC pathway.     

Swine chromosomes: flow sorting and spot blot hybridization

Flow cytometry analysis was applied to swine chromosomes prepared from phytohemagglutinin (PHA) stimulated peripheral blood lymphocytes. Flow karyotypes from both sexes and from t(3;7) translocation carrier females were obtained. A certain number of chromosome pairs could be assigned to various peaks. In fact, 13 peaks were observed for 18 autosomal pairs plus X and Y. Moreover, abnormalities owing to the t(3;7) translocation were readily observable. The number of base pairs for chromosomes associated with the various peaks was estimated by comparison with human flow karyotypes. The following four peaks were thus sorted: the peak assumed to represent the translocated chromosome 7 plus the normals associated with it; the corresponding peak from a normal swine; the peak assumed to contain among others the normal chromosome 7; and finally the peak corresponding to swine chromosome 1. Chromosomes of each peak were collected on Pall Biodyne membrane. Following appropriate denaturation and prehybridization, the four samples were hybridized with a human leucocyte antigen (HLA) class I 32P-labelled cDNA probe, representing most of the coding sequence of the HLA B7 gene. The results confirmed previous data from other techniques that assigned the swine MHC(SLA) to chromosome 7. Subsequently, sorted samples were hybridized with a porcine genomic Interferon alpha probe in order to confirm the mapping of this gene family on porcine chromosome 1.     

A novel porcine gene, POT1, differentially expressed in the longissimus muscle tissues from Wujin and Large White pigs

The mRNA differential display technique was performed to investigate the differences of gene expression in the longissimus muscle tissues from Wujin and Large White pigs. One novel gene differentially expressed was identified through quantitative real time PCR and the cDNA complete sequence was then obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 507 amino acids that shares high homology with the protection of telomeres 1 isoform 4 (POT1) of human (86%)-so that this gene can be defined as swine POT1 gene. This gene is structured in 12 exons and 11 introns as revealed by computer-assisted analysis. The tissue expression analysis indicated that the swine POT1 gene is differentially expressed in tissues including muscle, heart, liver, fat, kidney, lung, pancreas and spleen. Our experiment is the first to establish the primary foundation for further research on the swine POT1 gene.     

Interrelationships of platelet-derived growth factor isoform-induced changes in c-fos expression, intracellular free calcium, and mitogenesis

Both increases in c-fos proto-oncogene expression and intracellular free calcium ([Ca2+]i) have been implicated as necessary components of the signal transduction pathway by which platelet-derived growth factor (PDGF) stimulates DNA synthesis in cultured BALB/c3T3 fibroblasts. To determine the interrelationship between PDGF-induced increases in c-fos proto-oncogene expression and [Ca2+]i, purified, recombinant BB and AA homodimeric isoforms of PDGF were used to evaluate the dose-response relationships and mechanisms of growth factor-induced changes in these two parameters as well as DNA synthesis. Concentration-dependent increases in [Ca2+]i, c-fos expression, and [3H]thymidine incorporation were observed with both BB and AA PDGF isoforms. BB PDGF was consistently more potent and efficacious than the AA isoform in eliciting a given response. The [Ca2+]i dependency of PDGF-induced increases in c-fos expression and DNA synthesis was determined by pretreatment of cells with agents that inhibit increases in [Ca2+]i: BAPTA, Quin-2, and TMB-8. Under these conditions, PDGF-induced DNA synthesis was blocked, whereas c-fos expression was enhanced. Conversely, in cells made deficient in protein kinase C (PKC) activity by prolonged treatment with phorbol ester, BB and AA PDGF-induced c-fos expression was inhibited by 75-80%, while PDGF-induced increases in [Ca2+]i and DNA synthesis were unaffected or enhanced. Additionally, the PKC-independent component of PDGF-stimulated c-fos expression was found to be independent of increases in [Ca2+]i. These data suggest that 1) both BB and AA PDGF isoforms elicit alterations in [Ca2+]i and c-fos proto-oncogene expression through the same or similar mechanisms in BALB/c3T3 fibroblasts, 2) PDGF-stimulated increases in [Ca2+]i are not required for c-fos expression, and 3) distinct pathways regulate PDGF-induced c-fos expression and mitogenesis, with c-fos expression being substantially PKC-dependent yet [Ca2+]i-independent, while mitogenesis is [Ca2+]i-dependent yet PKC-independent.     

Molecular cloning, characterization, and chromosomal assignment of porcine cationic amino acid transporter-1

We have cloned and characterized the gene encoding the porcine cationic amino acid transporter, member 1 (CAT-1) (HGMW-approved gene symbol SLC7A1) from porcine pulmonary artery endothelial cells. The porcine SLC7A1 encodes 629 deduced amino acid residues showing a higher degree of sequence similarity with the human counterpart (91.1%) than with the rat (87.3%) and mouse (87.6%) counterparts. Confocal microscopic examination of porcine CAT-1-GFP-expressing HEK293 cells revealed that porcine CAT-1 localizes on the plasma membrane. Amino acid uptake studies in Xenopus oocytes injected with cRNA encoding this protein demonstrated transport properties consistent with system y(+). Radiation hybrid mapping data indicate that the porcine SLC7A1 maps to the distal end of the short arm of pig chromosome 11 (SSC11). This map location is consistent with the known conservation of genome organization between human and pig and provides further confirmation that we have characterized the porcine orthologue of the human SLC7A1.     

The porcine skeletal muscle ryanodine receptor gene structure coding region 1 to 10 614 harbouring 71 exons

The skeletal muscle ryanodine receptor (RYR1) belongs to a family of calcium release channels that are expressed in different tissues. The RYR1 gene is one of the largest genes characterized, so far, containing a 15 253 nucleotide ORF in swine. To study the genomic organization of the porcine skeletal muscle ryanodine receptor gene we have isolated seven genomic fragments spanning 72.7 kb of chromosomal DNA of chromosome 6q12. This region harbours exons 1 to 71 coding for 3538 amino acids (69.6%) of the ryanodine receptor 1.