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Trott JF, Freking BA, Hovey RC. Variation in the coding and 3′ untranslated regions of the porcine prolactin receptor short form modifies protein expression and function. Anim Genet 2013; 45:74-86. [DOI: 10.1111/age.12100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Josephine F. Trott
- Department of Animal Science; University of California, Davis; One Shields Ave Davis CA 95616 USA
| | - Bradley A. Freking
- USDA, ARS; US Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - Russell C. Hovey
- Department of Animal Science; University of California, Davis; One Shields Ave Davis CA 95616 USA
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2
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3
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Abstract
Swine genomic DNA segments containing repetitive sequences were isolated from a porcine genomic library using genomic DNA as a probe. Three fragments containing the repetitive sequences from two of the primary phage clones were subcloned for sequence analysis, which revealed six new PRE-1 repetitive families other than those reported earlier by Singer et al. (Nucleic Acids Research 15, 2780, 1987). The frequency of the repetitive sequences in the swine genome was estimated at 2 x 10(6) per diploid genome. Sequence analysis revealed similarities between these repetitive sequences and that of arginine-tRNA gene.
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Affiliation(s)
- H Takahashi
- Department of Animal Breeding and Genetics, National Institute of Animal Industry, Tsukuba, Japan
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4
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Liu JJ, Ran XQ, Li S, Feng Y, Wang JF. Polymorphism in the first intron of follicle stimulating hormone beta gene in three Chinese pig breeds and two European pig breeds. Anim Reprod Sci 2009; 111:369-75. [PMID: 18436398 DOI: 10.1016/j.anireprosci.2008.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 11/22/2007] [Accepted: 03/14/2008] [Indexed: 11/18/2022]
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5
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The negative effects of exogenous DNA binding on porcine spermatozoa are caused by removal of seminal fluid. Theriogenology 2008; 70:1288-96. [DOI: 10.1016/j.theriogenology.2008.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Yu L, Zhang YP. Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals. Mamm Genome 2005; 16:651-60. [PMID: 16245022 DOI: 10.1007/s00335-004-2456-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 05/20/2005] [Indexed: 10/25/2022]
Abstract
An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed element (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR element is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.
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Affiliation(s)
- Li Yu
- Laboratory of Molecular Biology of Domestic Animals, and Cellular and Molecular Evolution, Kunming Institute of Zoology, Kunming, 650223, China
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7
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Wetton JH, Tsang CSF, Roney CA, Spriggs AC. An extremely sensitive species-specific ARMs PCR test for the presence of tiger bone DNA. Forensic Sci Int 2004; 140:139-45. [PMID: 15017992 DOI: 10.1016/j.forsciint.2003.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The survival of the tiger (Panthera tigris) is seriously threatened by poaching to provide raw materials for Traditional Chinese Medicines (TCMs). Most highly prized are the tiger's bones, which are used in combination with other animal and plant derivatives in pills and plasters for the treatment of rheumatism and other ailments. Hundreds of patent remedies have been produced which claim to contain tiger bone, but proof of its presence is needed, if legislation prohibiting the trade in endangered species is to be enforced. A highly sensitive tiger-specific real-time PCR assay has been developed to address this problem. Using primers specific to the tiger mitochondrial cytochrome b gene, successful amplification has been reliably achieved from blood, hair and bone as well as from a range of TCMs spiked with 0.5% tiger bone. Although capable of detecting fewer than 10 substrate molecules, the seven varieties of TCM pills and plasters tested showed no detectable trace of tiger DNA before spiking. Furthermore, sequencing several "tiger bone" fragments seized from TCM shops has shown that they actually originated from cattle and pigs. The potential effects of traditional bone preparation methods, evidence that much lower concentrations are used than alleged on TCM packaging, and substitution of bones from other species all suggest a low likelihood of detecting tiger DNA in patent medicines. Despite this, the basic methods have been thoroughly proven and can be readily applied to derivatives from other CITES protected species providing a rapid and highly sensitive forensic test for species of origin. Potential applications to the monitoring of wild populations are demonstrated by the successful identification of shed hairs and faecal samples.
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Affiliation(s)
- Jon H Wetton
- Forensic Science Service, R and D, Solihull, UK.
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8
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Wetton JH, Tsang CSF, Roney CA, Spriggs AC. An extremely sensitive species-specific ARMS PCR test for the presence of tiger bone DNA. Forensic Sci Int 2002; 126:137-44. [PMID: 12084490 DOI: 10.1016/s0379-0738(02)00045-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The survival of the tiger (Panthera tigris) is seriously threatened by poaching to provide raw materials for traditional Chinese medicines (TCMs). Most highly prized are the tiger's bones, which are used in combination with other animal and plant derivatives in pills and plasters for the treatment of rheumatism and other ailments. Hundreds of patent remedies have been produced which claim to contain tiger bone, but proof of its presence is needed if legislation prohibiting the trade in endangered species is to be enforced.A highly sensitive tiger-specific real-time PCR assay has been developed to address this problem. Using primers specific to the tiger mitochondrial cytochrome b gene, successful amplification has been reliably achieved from blood, hair and bone as well as from a range of TCMs spiked with 0.5% tiger bone. Although capable of detecting fewer than 10 substrate molecules, the seven varieties of TCM pills and plasters tested showed no detectable trace of tiger DNA before spiking. Furthermore, sequencing several "tiger bone" fragments seized from TCM shops has shown that they actually originated from cattle and pigs. The potential effects of traditional bone preparation methods, evidence that much lower concentrations are used than alleged on TCM packaging, and substitution of bones from other species all suggest a low likelihood of detecting tiger DNA in patent medicines. Despite this, the basic methods have been thoroughly proven and can be readily applied to derivatives from other Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) protected species, providing a rapid and highly sensitive forensic test for species of origin. Potential applications to the monitoring of wild populations are demonstrated by the successful identification of shed hairs and faecal samples.
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Affiliation(s)
- Jon H Wetton
- Forensic Science Service, R&D, Trident Court, Birmingham Business Park, Solihull B37 7YN, UK.
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9
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Zhang G, Hiraiwa H, Yasue H, Wu H, Ross CR, Troyer D, Blecha F. Cloning and characterization of the gene for a new epithelial beta-defensin. Genomic structure, chromosomal localization, and evidence for its constitutive expression. J Biol Chem 1999; 274:24031-7. [PMID: 10446172 DOI: 10.1074/jbc.274.34.24031] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian beta-defensins are endogenous cysteine-rich peptide antibiotics that are produced either by epithelial cells lining the respiratory, digestive, and urogenital tracts or by granulocytes and macrophages. A growing body of evidence has implicated these peptides in host defense, particularly mucosal innate immunity. We previously reported the cloning of the full-length cDNA for a porcine beta-defensin (pBD-1), which was found to be expressed throughout the airway and oral mucosa. Here, we provide the structural organization of the pBD-1 gene, showing that the entire gene spans approximately 1.9 kilobases with two short exons separated by a 1.5-kilobase intron. Fluorescence in situ hybridization mapped the pBD-1 gene to porcine chromosome 15q14-q15. 1 within a region of conserved synteny to the chromosomal locations of human and mouse alpha- and beta-defensins. We also provide several independent lines of evidence showing that the pBD-1 gene is expressed constitutively during inflammation and infection, despite its resemblance to many inducible epithelial beta-defensins in amino acid sequence, genomic structure, and sites of expression. First, stimulation of primary porcine tongue epithelial cells with lipopolysaccharide, tumor necrosis factor-alpha, and interleukin (IL)-1beta failed to up-regulate the expression of pBD-1 mRNA. Second, pBD-1 gene expression was not enhanced in either digestive or respiratory mucosa of pigs following a 2-day infection with Salmonella typhimurium or Actinobacillus pleuropneumoniae. Last, direct transfection of the pBD-1 gene promoter into NIH/3T3 cells showed no difference in reporter gene activity in response to stimulation by lipopolysaccharide and IL-1beta. The constitutive expression of pBD-1 in airway and oral mucosa, which is consistent with a lack of consensus binding sites for nuclear factor-kappaB or NF-IL-6 in its promoter region, suggests that it may play a surveillance role in maintaining the steady state of microflora on mucosal surfaces.
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Affiliation(s)
- G Zhang
- Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506, USA
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10
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Abstract
We have cloned and characterized a single-copy DNA sequence from the porcine alpha-1,3-galactosyltransferase gene that corresponds to a 547-base pair intron separating exons 3 and 4 of the protein coding domain. Polymerase chain reaction amplification of this sequence from flanking oligonucleotides generates a species-specific DNA probe (pgt34) capable of recognizing 50 pg chimeric template DNA at a pig to human cellular ratio of 1/10,000. Homologous DNA sequence is not identified in the macaque, baboon, or human genome by Southern hybridization. Analysis of a discordant model of pig to baboon xenotransplantation demonstrates peripheral blood microchimerism in the presence of a functioning pig kidney xenograft and persistence of microchimerism in lymphatic tissue after graft removal. This probe should be useful for tracking the fate of porcine cells in patients undergoing xenotransplantation of whole organs or free tissues such as pancreatic islet cells and should facilitate studies of microchimerism in experimental models of pig to monkey xenotransplantation.
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Affiliation(s)
- C W Hoopes
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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11
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Wen G, Leeb T, Reinhart B, Schmoelzl S, Brenig B. The porcine skeletal muscle ryanodine receptor gene structure coding region 1 to 10614 harbouring 71 exons. Anim Genet 1996; 27:297-304. [PMID: 8930069 DOI: 10.1111/j.1365-2052.1996.tb00973.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
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 15253 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.
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Affiliation(s)
- G Wen
- Institute of Veterinary Medicine, University of Goettingen, Germany
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12
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Zijlstra C, Bosma AA, de Haan NA, Mellink C. Construction of a cytogenetically characterized porcine somatic cell hybrid panel and its use as a mapping tool. Mamm Genome 1996; 7:280-4. [PMID: 8661693 DOI: 10.1007/s003359900083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A new panel of cytogenetically characterized pig-rodent somatic cell hybrids was constructed and tested for twelve microsatellite markers with PCR. Cytogenetic characterization of hybrids was accomplished by fluorescence painting and GTG-banding of metaphase chromosomes. The panel consists of 15 independent pig-hamster and 6 independent pig-mouse cell lines. In the panel, all pig autosomes and the X Chromosome (Chr) are represented, and it is informative for all chromosome pairs except 2-14, 2-15, 3-9, 14-15, 14-16, and 16-17. The microsatellites tested were S0022, S0023, S0084, S0098, S0112, S0113, S0114, S0115, S0117, S0118, S0119, and S0120. The PCR results obtained in the 21 hybrids were compared with the cytogenetic data and analyzed for concordancy and correlation. Eight microsatellites could be assigned to specific pig chromosomes, confirming seven assignments based on linkage analysis.
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Affiliation(s)
- C Zijlstra
- Department of Cell Biology and Histology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80.157, 3508 TD Utrecht, The Netherlands
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13
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Leeb T, Brenig B. Structural analysis of the porcine skeletal muscle ryanodine receptor gene coding region 3385 to 4623. Mamm Genome 1996; 7:152-4. [PMID: 8835535 DOI: 10.1007/s003359900038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- T Leeb
- Institute of Veterinary Medicine, University of Goettingen, Germany
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14
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Thomsen PD, Miller JR. Pig genome analysis: differential distribution of SINE and LINE sequences is less pronounced than in the human and mouse genomes. Mamm Genome 1996; 7:42-6. [PMID: 8903727 DOI: 10.1007/s003359900010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The distribution of SINE and LINE sequences in the pig genome was examined by fluorescence in situ hybridization (FISH), interspersed repeat PCR, and restriction analysis of high molecular weight DNA. FISH revealed a largely uniform hybridization to the euchromatic chromosome regions with both interspersed repeats, although a bias toward the G-bands was observed for the LINE probe. Southern blots of inter-SINE and inter-LINE PCR products showed strong hybridization to LINE and SINE probes, respectively. High molecular weight DNA derived from a pig x hamster hybrid cell line was cut with a panel of G + C and A + T rich rare cutter restriction enzymes, then run on a pulsed field gel and Southern blotted. Sequential hybridization with SINE and LINE probes showed that SINE hybridization was to relatively low molecular weight fragments with the G + C rich enzymes, whereas the LINE probe gave hybridization to significantly larger fragments produced by these enzymes. DNA samples digested with A + T rich enzymes gave essentially similar patterns with SINE and LINE probes. We conclude that the pattern of differential distribution of SINEs and LINEs, which has been described in man and mouse, does exist in the pig but is much less pronounced.
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Affiliation(s)
- P D Thomsen
- Department of Anatomy and Physiology, The Royal Veterinary and Agriculural University, Frederiksberg C, Denmark
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15
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Schmid CW. Alu: structure, origin, evolution, significance and function of one-tenth of human DNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 53:283-319. [PMID: 8650306 DOI: 10.1016/s0079-6603(08)60148-8] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C W Schmid
- Section of Molecular and Cellular Biology, University of California, Davis 95616, USA
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16
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Harumi T, Kimura M, Yasue H. Survey on swine SINEs (PRE-1) as candidates for SSCP markers in genetic linkage analysis. Anim Genet 1995; 26:403-6. [PMID: 8572362 DOI: 10.1111/j.1365-2052.1995.tb02691.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Of 310 random cosmid clones, 216 were positive for PRE-1 sequences by Southern hybridization. Thirty nine sub-fragments positive for the PRE-1 sequences were cloned from independent cosmid clones, and sequenced, with 17 complete PRE-1 elements found. Seven PRE-1 loci were amplified by polymerase chain reaction using genomic DNA of 12 unrelated pigs as template. The amplified fragments were then subjected to an analysis of single strand conformation polymorphism, with all the loci being polymorphic.
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Affiliation(s)
- T Harumi
- Animal Genome Research Group, National Institute of Animal Industry, Ibaraki, Japan
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17
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Thomsen PD, Zhdanova NS. Reverse painting for identification of pig chromosomes in hybrid cell lines: assignment of the HOXB and the TK1 gene to pig chromosome 12p. Mamm Genome 1995; 6:670-2. [PMID: 8535081 DOI: 10.1007/bf00352380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- P D Thomsen
- Department of Anatomy and Physiology, Royal Veterinary and Agricultural University, Frederiksberg C, Denmark
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18
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Jobse C, Buntjer JB, Haagsma N, Breukelman HJ, Beintema JJ, Lenstral JA. Evolution and recombination of bovine DNA repeats. J Mol Evol 1995. [DOI: 10.1007/bf01215174] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Alexander LJ, Rohrer GA, Stone RT, Beattie CW. Porcine SINE-associated microsatellite markers: evidence for new artiodactyl SINEs. Mamm Genome 1995; 6:464-8. [PMID: 7579888 DOI: 10.1007/bf00360655] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Approximately 24% (170/710) of porcine (dG-dT)n.(dC-dA)n microsatellites isolated in our laboratory are associated with a previously described porcine Short Interdispersed Element (SINE) termed PRE-1 SINE. Another 5.6% (40/710) of the microsatellites were adjacent to two previously unidentified SINE sequences, which we have designated ARE-1P (Artiodactyl Repetitive Element-1 Porcine) and ARE-2P. The ARE repeats were also found in bovine microsatellite and genomic sequences in the GenBank database. Genotypic information was obtained from 68.9% of primers where at least one primer sequence was obtained from the PRE-1 SINE and 66.6% of primer pairs designed from the ARE SINEs. The use of primers derived from SINEs significantly increases the number of primer pairs available for genetic linkage studies in swine.
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Affiliation(s)
- L J Alexander
- United States Department of Agriculture, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA
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20
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Raisonnier A, Etienne J, Arnault F, Brault D, Noé L, Chuat JC, Galibert F. Comparison of the cDNA and amino acid sequences of lipoprotein lipase in eight species. Comp Biochem Physiol B Biochem Mol Biol 1995; 111:385-98. [PMID: 7613763 DOI: 10.1016/0305-0491(95)00006-t] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
By aligning nucleotide and amino acid sequences of lipoprotein lipase in eight species (man, pig, cow, sheep, mouse, rat, guinea-pig and chicken), we found that the main domains (catalytic, N-glycosylation and putative heparin binding sites) are well conserved. The longest identical amino acid chain was encoded by a sequence between the end of exon 2 and the beginning of exon 3, emphasizing the importance of this region which encodes the beta 5-loop of the active site, among other domains. Exon 10 is entirely untranslated in the seven mammals studied here and contains species-characteristic deletions, insertions or elements rich in A or A + T. In chicken, the beginning of exon 10 is translated. These eight previously unreported alignments could be a useful tool for further studies on LPL function.
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Abstract
Genomic clones encoding pig phosphoglucose isomerase (PGI) have been isolated and partially sequenced. The gene (Pgi) contains 18 exons, 17 introns and spans about 32 kb. This structure is partially conserved between plant and animal. A major transcription start point (tsp) has been identified 74 nucleotides (nt) upstream from the AUG. The nt sequence around the tsp is very G+C rich; a 5'-ATAAA sequence, as well as four putative Sp1-binding sites, are present. In the 3'-flanking region, an AATAAA signal has been identified. Extending from the 5'-flanking region to the first intron, a 0.6-kb CpG island has been identified. The Pgi structural gene contains several DNA repetitive elements in its non-coding regions.
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Affiliation(s)
- V Claes
- Department of Molecular Biology and Animal Physiology, Faculty of Agronomy, Gembloux, Belgium
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22
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Davies W, Høyheim B, Chaput B, Archibald AL, Frelat G. Characterization of microsatellites from flow-sorted porcine chromosome 13. Mamm Genome 1994; 5:707-11. [PMID: 7873881 DOI: 10.1007/bf00426077] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Porcine flow-sorted Chromosome (Chr) 13 was PCR amplified with primers based on porcine short interspersed element (SINE) sequences. The product was cloned, gridded in microtiter plates, and screened with a [GT]10 oligonucleotide which gave 45 positive clones. Sequencing of these clones showed that 36 were unique, and 26 [GT]n microsatellites were characterized. Six other simple repeat sequences, the majority of which were associated with the 3' end of the SINE sequence, were also detected. Twenty-one primers sets were selected, and 13 of these detected useful polymorphisms in the grandparents (n = 26) of the European porcine mapping collaboration (PiGMaP) reference families. These 13 markers were mapped in the "PiGMaP" reference families, and a two-point linkage analysis was performed. The Lod scores indicated that three of the markers were not linked and the remaining 11 formed two linkage groups of two and nine markers respectively. The larger linkage group was also linked to the transferrin locus, permitting assignment of nine markers to porcine Chr 13.
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Affiliation(s)
- W Davies
- Norwegian College of Veterinary Medicine, Department of Biochemistry, Physiology and Nutrition, Oslo
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23
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Abstract
The pig chromosome complement of six different types of pig-rodent hybrid cell lines was examined by means of fluorescence in situ hybridization with a porcine SINE probe. The cell lines were obtained by fusing pig lymphocytes with cells of the Chinese hamster cell lines wg3h, BK14-150 and E36, and of the mouse cell lines NSO, PU and LMTK-. The hybrids were analysed with respect to: (1) the number of pig chromosomes, (2) the type of pig chromosomes, (3) the occurrence of pig-rodent chromosome translocations, and (4) the presence of pig chromosome fragments. The results show that the number of pig chromosomes varied within and among hybrid cell lines. The pig-hamster hybrids mainly retained nontelocentric pig chromosomes, whereas the pig-mouse hybrids also retained telocentric pig chromosomes. Pig-rodent chromosome translocations were found in all types of hybrids, but the incidence was in general low. Chromosome fragments were abundant in BK14-150 hybrids, and rare in most other hybrid cell lines. It is concluded that the SINE probe is a useful tool to make a preliminary characterization of the porcine chromosome complement of pig-rodent somatic cell hybrids. The results of this characterization can be used to select hybrids for further cytogenetic analysis. Furthermore, our data show that different rodent cell lines will have to be used as fusion partners for the production of hybrids when constructing a panel informative for all pig chromosomes.
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Affiliation(s)
- C Zijlstra
- Department of Cell Biology and Histology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
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24
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Abstract
PCR primers derived from porcine short and long interspersed repeat sequences were used to amplify DNA samples isolated from individual members of three-generation pig reference pedigrees. Subsequent high-resolution gel electrophoresis of both SINE and LINE-PCR products allowed direct visualisation of polymorphisms that segregated in a Mendelian manner. Additional polymorphisms were detected by Southern blotting of the gels described above followed by hybridization with simple sequence DNA. Genotyping by interspersed repeat-PCR exploits the natural architecture of the pig genome and allows the typing of polymorphisms by utilizing pre-existing sequence information.
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Affiliation(s)
- J R Miller
- Department of Immunology, Babraham Institute, Cambridge, UK
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25
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Frengen E, Thomsen PD, Schmitz A, Frelat G, Davies W. Isolation of region-specific probes from pig chromosome 6 by coincidence cloning. Mamm Genome 1994; 5:497-502. [PMID: 7949734 DOI: 10.1007/bf00369319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Coincidence cloning is a technique that permits the isolation of sequences common to two independent sources of complex DNA, and this method has been used to isolate a set of probes from a region of porcine Chromosome (Chr) 6 containing the loci for glucosephosphate isomerase (GPI) and the skeletal muscle calcium release channel (CRC). Porcine DNA was specifically PCR-amplified from a pig x hamster hybrid cell line containing the centromere region (p1.2-q1.2) of pig Chr 6 and other pig chromosome fragments by use of a porcine SINE specific primer with an EcoRI site in the 5'-end. Flow-sorted Chr 6 preparations were amplified with the same SINE primer, but with a SalI site in the 5'-end. The products were digested with EcoRI and SalI respectively, combined, denatured, and reannealed. The heteroduplex molecules, containing both an EcoRI and a SalI cohesive end, were selected by cloning in SalI/EcoRI-digested pUC13. Approximately 40% of the primary clones contained a single SalI/EcoRI-insert, indicating that they are coincidence clones. The average insert size was 1.4 kb. Fluorescence in situ hybridization of a pool of 34 coincidence clones to pig chromosomes showed a preferential labeling of the centromere region and of the q2.5-q2.7 region of pig Chr 6. Nineteen coincidence clones were hybridized to SINE-PCR products from flow-sorted pig Chr 6 and to pig x rodent hybrid cell lines. Eighteen clones gave positive signals correlated with the GPI/CRC content of the source DNAs.
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Affiliation(s)
- E Frengen
- Department of Biochemistry, Physiology and Nutrition, Norwegian College of Veterinary Medicine, Oslo
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26
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Ellegren H, Chowdhary B, Johansson M, Andersson L. Integrating the porcine physical and linkage map using cosmid-derived markers. Anim Genet 1994; 25:155-64. [PMID: 7943949 DOI: 10.1111/j.1365-2052.1994.tb00104.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An essential part in the development of informative linkage maps is to include genetic markers that have been anchored by physical mapping. Here a set of 18 porcine cosmid-derived genetic markers are reported that have been mapped by linkage analysis, and that also have been physically localized by fluorescence in situ hybridization (FISH). Three different strategies were used to establish polymorphic markers from the cosmid clones. Firstly, dinucleotide microsatellite loci were derived by sequencing cosmid subclones containing (CA)n repeats. Secondly, variable SINE 3' poly(A) tracts (SINEVA) were identified by direct SINE-PCR amplification of cosmid clones. Thirdly, the cosmids were used in Southern blot hybridization to detect restriction fragment length polymorphisms (RFLPs). Compared with the most recent consensus compilation of the porcine gene map, the present assignment of markers to chromosomes 2p, 3, 4, 10, 12q, and 16 represents the first loci mapped to these chromosomes, for which linkage as well as in situ data are now available.
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Affiliation(s)
- H Ellegren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala
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Thomsen PD, Winterø AK, Bosma A, Fredholm M. A porcine repeat family located on 3p14 and distal to the rRNA gene cluster on chromosome 10. Mamm Genome 1994; 5:244-6. [PMID: 8012117 DOI: 10.1007/bf00360555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- P D Thomsen
- Department of Anatomy and Physiology, Royal Veterinary and Agricultural University, Frederiksberg C, Denmark
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Ellegren H. Abundant (A)n.(T)n mononucleotide repeats in the pig genome: linkage mapping of the porcine APOB, FSA, ALOX12, PEPN and RLN loci. Anim Genet 1993; 24:367-72. [PMID: 7904801 DOI: 10.1111/j.1365-2052.1993.tb00342.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A computer analysis revealed that the mononucleotide repeat (A)n.(T)n is about five times as common as (CA)n.(GT)n repeats in the porcine genome, with frequency estimates of one every 7kb and 30kb, respectively. Seven mononucleotide repeats with n = 12-25 located close to coding sequences were analysed for polymorphism using polymerase chain reaction (PCR) amplification and polyacrylamide gel electrophoresis. All loci were variable with 3-6 alleles and heterozygosities of 0.26-0.69 based on investigation of 10 unrelated pigs (two wild boars and eight domestic sows). Repeat length correlated with degree of polymorphism. A comparison with (CA)n.(GT)n polymorphisms suggested that the number of repeat units rather than the total length of the repeat region is the common denominator that governs polymorphism at both mono- and dinucleotide repeat loci. (A)n.(T)n polymorphisms allowed linkage mapping of relaxin to chromosome 1, apolipoprotein B to chromosome 3, aminopeptidase N to chromosome 7, arachidonate 12-lipoxygenase to chromosome 12, and follistatin to chromosome 16. The rich abundance of potentially informative (A)n.(T)n repeats will increase the chances of finding a PCR-based marker near any DNA sequence of interest.
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Affiliation(s)
- H Ellegren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala
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A novel and atypical type one interferon gene expressed by trophoblast during early pregnancy. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)36579-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Lenstra JA, van Boxtel JA, Zwaagstra KA, Schwerin M. Short interspersed nuclear element (SINE) sequences of the Bovidae. Anim Genet 1993; 24:33-9. [PMID: 8498711 DOI: 10.1111/j.1365-2052.1993.tb00916.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
DNA sequences from Bovidae (cattle, goats and sheep) in the EMBL nucleotide database contain several short interspersed repeated sequences (SINEs). Three different SINEs have been found: Bov-A2, containing two 115-bp A elements; Bov-tA, a tRNA pseudogene coupled to an A element; and Bov-B of 560 bp or less and partially homologous to the A element. Bov-A2, Bov-tA and Bov-B occupy about 1.8%, 1.6% and 0.5%, respectively, of the bovine genome as represented in the nucleotide database. Apart from a tRNA-like sequence in both Bov-tA and the porcine SINEs, there was no similarity with the porcine SINEs. Apparently, the artiodactyle SINEs were established after the divergence leading to the Suidae and Bovidae but before the radiation within these families. Oligonucleotides were designed for a specific amplification of DNA from Bovidae.
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Affiliation(s)
- J A Lenstra
- Institute of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht, The Netherlands
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Ellegren H. Variable SINE 3' poly(A) sequences: an abundant class of genetic markers in the pig genome. Mamm Genome 1993; 4:429-34. [PMID: 8397020 DOI: 10.1007/bf00296816] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Previous studies on human DNA have shown that the 3' poly(A) tracts of Alu elements may display considerable genetic polymorphism. To explore whether this marker type is generally applicable in mammalian genomes, I analyzed porcine SINEs. A database screening revealed 17 porcine sequences with significant homology to a previously identified pig SINE. The occurrence in the database suggested a SINE frequency of one copy every 12 kb of pig DNA. All SINEs contained a 3' poly(A) tract with an average of 12 uninterrupted adenines. The repetitive regions were analyzed for polymorphism by locus-specific PCR amplification. Allelic length variation (two to five alleles among 10 pigs) was found at 8 out of 10 loci investigated, in most cases probably because of varying number of iterated adenine residues. There was a positive relationship between repeat length and the degree of polymorphism. Stable Mendelian inheritance was documented in 200 meioses each at four loci. The high genomic frequency of SINEs implies that a potentially informative marker may be found near any gene or in any cosmid clone. These SINE 3' poly(A) polymorphisms, termed SINEVA [SINE variable poly(A)s], thus provide an abundant and useful class of genetic marker in mammalian genomes.
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Affiliation(s)
- H Ellegren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala
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Miller JR, Archibald AL. 5' and 3' SINE-PCR allows genotyping of pig families without cloning and sequencing steps. Mamm Genome 1993; 4:243-6. [PMID: 8507977 DOI: 10.1007/bf00417429] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A microsatellite-containing clone, isolated from a pig Chromosome (Chr) 1-specific library was characterized by sequencing and computer analysis. The (CA)17 microsatellite motif was located at the 3' end of a short interspersed element (SINE) sequence at the position normally occupied by the oligo (A) stretch. Further computer analysis indicated that 12% of published pig SINE sequences contain dinucleotide repeat motifs adjacent to their 3' ends. By performing PCR with a single SINE primer in combination with a panel of arbitrarily selected unique primers, we have demonstrated that, as in human, polymorphisms can be detected and typed in pig family DNAs. A large number of SINE primer x unique primer combinations have been screened for the ability to detect polymorphisms in pig reference family DNAs. This approach does not require prior sequence information other than that of the pig SINE. We have also found polymorphisms at the 5' ends of pig SINE sequences by similar methods, but with a primer facing out to the 5' end of the SINE.
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Affiliation(s)
- J R Miller
- Agricultural and Food Research Council Institute of Animal Physiology and Genetics Research Cambridge Research Station, UK
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Kaukinen J, Varvio SL. Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR. Nucleic Acids Res 1992; 20:2955-8. [PMID: 1377817 PMCID: PMC312422 DOI: 10.1093/nar/20.12.2955] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
During a search of polymorphic microsatellites for bovine genome mapping, we found that microsatellites often occur as tails of artiodactyl C-A retroposon elements. In this element, C (85bp) is a tRNA derivative, while A (117bp) is of unknown origin. The A element also occurs as dimer element with a connecting 27bp linker sequence comprising hexanucleotide CACTTT repeats. In 10 clones (45% of those selected deliberately for dinucleotide repeats), the microsatellite motif is associated with the C-A retroposon. In 50% of 44 database artiodactyl C-A sequences, the element also has a microsatellite tail. The microsatellite is usually a simple (CA)n repeat, but in some cases it is an apparent derivative of the linker sequence CACTTT. All but one of 33 database dimer elements have trinucleotide repeat tails (AGC)n, n = 1-9. Microsatellites, retroposons, and their truncated versions (C and/or A) often occur as clusters. We derived the consensus sequence (202bp) of the C-A element, and designed four primers for inter-SINE amplification with the aim of finding SINEmorph polymorphisms. The method is potentially powerful for rapidly producing polymorphic markers for artiodactyl genome mapping.
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Affiliation(s)
- J Kaukinen
- Institute of Biotechnology, University of Helsinki, Finland
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Abstract
One of the more widely studied simple repeat sequences in the mammalian genome is the (dG-dT)n.(dC-dA)n dinucleotide repeat sequence. As these repeats are highly polymorphic and fairly evenly distributed in diverse mammalian genomes, they constitute a very powerful tool for genetic mapping in a wide variety of species. So far, the knowledge about repeat sequences in the porcine genome is sparse and only a few areas of this genome have been sequenced. We have isolated and characterized 108 porcine (dG-dT)n.(dC-dA)n sequences and studied the distribution of these, both by investigating random clones and by performing in situ hybridization. A remarkable correlation between humans and pigs was found with respect to the structure, to the number of repeat blocks, and to the chromosomal distribution.
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Affiliation(s)
- A K Winterø
- Department of Animal Production and Animal Health, Royal Veterinary and Agricultural University, Frederiksberg, Denmark
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