Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region

Immunogenetics

Volumn 57, Issue 11, 2005, Pages 864-873

  Ando, Asako ^a   Shigenari, Atsuko ^a   Kulski, Jerzy K ^a,b   Renard, Christine ^c   Chardon, Patrick ^c   Shiina, Takashi ^a   Inoko, Hidetoshi ^a  

^a TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^b MURDOCH UNIVERSITY   (Australia)

^c DIF   (France)

Author keywords

MHC class I region; Non class I genes; Olfactory receptor; Ring finger related family; Sequencing analysis; Swine

Indexed keywords

ANTIGEN; HLA F ANTIGEN; HLA J ANTIGEN; SWINE LEUKOCYTE ANTIGEN 11; SWINE LEUKOCYTE ANTIGEN 5; SWINE LEUKOCYTE ANTIGEN 9; SWINE LEUKOCYTE ANTIGEN CLASS 1; TRIPARTITE MOTIF 15; UNCLASSIFIED DRUG;

ARTICLE; GENE CLUSTER; GENE SEQUENCE; NUCLEOTIDE SEQUENCE; OLFACTORY RECEPTOR; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SWINE; TELOMERE; ZINC FINGER MOTIF;

AMINO ACIDS; ANIMALS; BASE COMPOSITION; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONSENSUS SEQUENCE; CONTIG MAPPING; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYSICAL CHROMOSOME MAPPING; RECEPTORS, ODORANT; SEQUENCE HOMOLOGY; SWINE;

SUS SCROFA;

EID: 29144444503     PISSN: 00937711     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00251-005-0053-6     Document Type: Article

References (44)

1. Amadou C (1999) Evolution of the Mhc class I region: the framework hypothesis. Immunogenetics 49:362-367
2. Amadou C, Younger RM, Sims S, Mathews LH, Rogers J, Kumanovics A, Ziegler A, Beck S, Lindahl KF (2003) Coduplication of olfactory receptor and MHC class I genes in the mouse major histocompatibility complex. Hum Mol Genet 12:3025-3040
3. Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, Shigenari A, Yamagata T, Kulski JK, Naruse TK, Fujimori Y, Fukuzumi Y, Yamazaki M, Tashiro H, Iwamoto C, Umehara Y, Imanishi T, Meyer A, Ikeo K, Gojobori T, Bahram S, Inoko H (2003) Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A 100:7708-7713
4. Beck TW, Menninger J, Murphy WJ, Nash WG, O'Brien SJ, Yuhki N (2005) The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 56:702-709
5. Bernardi G (1993) The isochore organization of the human genome and its evolutionary history - a review. Gene 135:57-66
6. Chardon P, Renard C, Vaiman M (1999a) The major histocompatibility complex in swine. Immunol Rev 167:179-192
7. Chardon P, Rogel-Gaillard C, Peelman L, Yerle M, Verten FW, Renard C, Vaiman M (1999b) Physical organization of the pig major histocompatibility complex class II region. Immunogenetics 50:344-348
8. Chardon P, Renard C, Rogel-Gaillard C, Vaiman M (2000) The porcine major histocompatibility complex and related paralogous regions: a review. Genet Sel Evol 32:109-128
9. Chardon P, Rogel-Gaillard C, Cattolico L, Duprat S, Vaiman M, Renard C (2001) Sequence of the pig major histocompatibility region containing all non-classical class I genes. Tissue Antigens 57:55-65
10. Deininger PL (1983) Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis. Anal Biochem 129:216-223
11. Gustafson AL, Tallmadge RL, Ramlachan N, Miller D, Bird H, Antcza DF (2003) An ordered BAC contig map of the equine major histocompatibility complex. Cytogenet Genome Res 102: 189-195
12. Havlickova M, Prezeau L, Duthey B, Bettler B, Pin JP, Blahos J (2002) The intracellular loops of the GB2 subunit are crucial for G-protein coupling of the heteromeric gamma-aminobutyrate B receptor. Mol Pharmacol 62:343-350
13. Hurt P, Walter L, Sudbrak R, Klages S, Muller I, Shiina T, Inoko H, Lehrach H, Gunther E, Reinhardt R, Himmelbauer H (2004) The genomic sequence and comparative analysis of the rat major histocompatibility complex. Genome Res 14:631-639
14. Kaupmann K, Huggel K, Heid J, Flor PJ, Bischoff S, Mickel SJ, MacMaster G, Ansdt C, Bittiger H, Froestl W et al (1997) Expression cloning of GABA(B) receptors uncovers similarity to metabotropic glutamate receptors. Nature 386:239-246
15. Kostia S, Ruohonen-Lehto M, Vainola R, Varvio SL (2000) Phylogenetic information in inter-SINE and inter-SSR fingerprints of the artiodactyla and evolution of the bov-tA SINE. Heredity 84:37-45
16. Kulski JK, Gaudieri S, Dawkins RL (2000) Using Alu J elements as molecular clocks to trace the evolutionary relationships between duplicated HLA class I segments. J Mol Evol 50:510-519
17. Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H (2002) Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol Rev 190:95-122
18. Kulski JK, Anzai T, Shiina T, Inoko H (2004) MHC class I duplicon structures, organization and evolution within the alpha block of the rhesus macaque. Mol Biol Evol 21:2079-2091
19. Kumanovics A, Takada T, Lindahl KF (2003) Genomic organization of the mammalian MHC. Annu Rev Immunol 21:629-657
20. Lai L, Kolber-Simonds D, Park KW, Cheong HT, Greenstein JL, Im GS, Samuel M, Bonk A, Rieke A, Day BN, Murphy CN, Carter DB, Hawley RJ, Prather RS (2002) Production of alpha-1,3-galactosyltaransferase knockout pigs by nuclear transfer cloning. Science 295:1089-1092
21. Meyer M, Gaudieri S, Rhodes DA, Trowsdale J (2003) Cluster of TRIM genes in the human MHC class I region sharing the B30.2 domain. Tissue Antigens 61:63-71
22. Mizuki N, Ando H, Kimura M, Ohno S, Miyata S, Yamazaki M, Tashiro H, Watanabe K, Ono A, Taguchi S, Sugawara C, Fukuzumi Y, Okumura K, Goto K, Ishihara M, Nakamura S, Yonemoto J, Kikuti YY, Shiina T, Chen L, Ando A, Ikemura T, Inoko H (1997) Nucleotide sequence analysis of the HLA class I region spanning the 237-kb segment around the HLA-B and - C genes. Genomics 42:55-66
23. Mungall AJ, Palmer SA, Sims SK, Edwards CA et al (2003) The DNA sequence and analysis of human chromosome 6. Nature 425:805-811
24. Peelman LJ, Chardon P, Vaiman M, Mattheeuws M, Van Zeveren A, Van de Weghe A, Bouquet Y, Campbell RD (1996) A detailed physical map of the porcine major histocompatibility complex (MHC) class III region: comparison with human and mouse MHC class III regions. Mamm Genome 7:363-367
25. Rabin M, Fries R, Singer DS, Ruddle FH (1985) Assignment of the porcine major histocompatibility complex to chromosome 7 by in situ hybridization. Cytogenet Cell Genet 39:206-209
26. Renard C, Vaiman M, Chiannikulchai N, Cattolico L, Robert C, Chardon P (2001) Sequence of the pig major histocompatibility region containing the classical class I genes. Immunogenetics 53:490-500
27. Renard C, Chardon P, Vaiman M (2003) The phylogenetic history of the MHC class I gene families in pig, including a fossil gene predating mammalian radiation. J Mol Evol 57:420-434
28. Rogel-Gaillard C, Bourgeaux N, Billault A, Vaiman M, Chardon P (1999) Construction of a swine BAC library: application to the characterization and mapping of porcine type C endoviral elements. Cytogenet Cell Genet 85:205-211
29. Sachs DH (1994) The pig as a potential xenograft donor. Vet Immunol Immunopathol 43:185-191
30. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
31. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 10: 577-586
32. Shigenari A, Ando A, Renard C, Chardon P, Shiina T, Kulski JK, Yasue H, Inoko H (2004) Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters. Immunogenetics 55:695-705
33. Shiina T, Tamiya G, Oka A, Yamagata T, Yamagata N, Kikkawa E, Goto K, Mizuki N, Watanabe K, Fukuzumi Y, Taguchi S, Sugawara C, Ono A, Chen L, Yamazaki M, Tashiro H, Ando A, Ikemura T, Kimura M, Inoko H (1998) Nucleotide sequencing analysis of the 146 kb segment around the IkBL and MICA genes at the centromeric end of the HLA class I region. Genomics 47:372-382
34. Shiina T, Inoko H, Kulski JK (2004) An update of the HLA genomic region, locus information and disease association: 2004. Tissue Antigens 64:631-649
35. Smith TP, Rohrer GA, Alexander LJ, Troyer DL, Kirby-Dobbels KR, Janzen MA, Cornwell DL, Louis CF, Schock, LB, Beattie CW (1995) Directed integration of the physical and genetic linkage maps of the swine chromosome 7 reveals that SLA spans the centromere. Genome Res 5:259-271
36. Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphrey SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J, Beck S (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Res 14:1176-1187
37. The MHC Sequencing Consortium (1999) Complete sequence and gene map of a human major histocompatibility complex (MHC). Nature 401:921-923
38. Velten F, Rogel-Gaillard C, Renard C, Pontarotti P, Tazi-Ahnini R, Vaiman M, Chardon P (1998) A first map of the porcine major histocompatibility complex class I region. Tissue Antigens 51: 183-194
39. Velten F, Renald C, Rogel-Gaillard C, Vaiman M, Schrezenmeir J, Chardon P (1999) Spatial arrangement of pig MHC class I sequences. Immunogenetics 49:919-930
40. Weissert R, Kuhle J, de Graaf KL, Wienhold W, Herrmann MM, Muller C, Forsthuber TG, Wiesmuller KH, Melms A (2002) High immunogenicity of intracellular myelin oligodendrocyte glycoprotein epitopes. J Immunol 169:548-556
41. Xu Y, Rothchild MF, Warmer CM (1992) Mapping of the SLA complex of the miniature swine mapping of the SLA gene complex by pulsed field gel electrophoresis. Mamm Genome 2:2-10
42. Younger RM, Amadou C, Bethel G, Ehlers A, Lindahl KF, Forbes S, Horton R, Milne S, Mungall AJ, Trowsdal F, Volz A, Ziegler A, Beck S (2001) Characterization of clustered MHC-linked olfactory receptor genes in human and mouse. Genome Res 11:519-530
43. Zhang X, Firestein S (2002) The olfactory receptor gene superfamily of the mouse. Nat Neurosci 5:124-133
44. Zhang J, Zhang L, Zhao S, Lee EY (1998) Identification and characterization of the human HCG V gene product as a novel inhibitor of protein phosphatase-1. Biochemistry 37:16728-16734