Genomic structure of the whole D-J-C clusters and the upstream region coding V segments of the TRB locus in pig

Developmental and Comparative Immunology

Volumn 33, Issue 10, 2009, Pages 1111-1119

  Eguchi Ogawa, Tomoko ^a,b   Toki, Daisuke ^b,c   Uenishi, Hirohide ^a,b  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b Animal Genome Research Program   (Japan)

^c Society for Techno Innovation of Agriculture Forestry and Fisheries   (Japan)

Author keywords

Gene duplication; Genome sequence; Swine; T cell receptor chain

Indexed keywords

T LYMPHOCYTE RECEPTOR BETA CHAIN; VANILLOID RECEPTOR 6;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; EXON; GENE CLUSTER; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; IMMUNOGENETICS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SWINE; T LYMPHOCYTE; UNINDEXED SEQUENCE;

SUIDAE; SUS; VERTEBRATA;

EID: 67650239125     PISSN: 0145305X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dci.2009.06.006     Document Type: Article

References (36)

1. Davis M.M., Boniface J.J., Reich Z., Lyons D., Hampl J., Arden B., et al. Ligand recognition by αβ T cell receptors. Annu Rev Immunol 16 (1998) 523-544
2. Davis M.M. T cell receptor gene diversity and selection. Annu Rev Biochem 59 (1990) 475-496
3. Rowen L., Koop B.F., and Hood L. The complete 685-kilobase DNA sequence of the human β T cell receptor locus. Science 272 (1996) 1755-1762
4. Allison T.J., Winter C.C., Fournie J.J., Bonneville M., and Garboczi D.N. Structure of a human γδ T-cell antigen receptor. Nature 411 (2001) 820-824
5. Conrad M.L., Pettman R., Whitehead J., McKinnel L., Davis S.K., and Koop B.F. Genomic sequencing of the bovine T cell receptor beta locus. Vet Immunol Immunopathol 87 (2002) 439-441
6. Antonacci R., Di Tommaso S., Lanave C., Cribiu E.P., Ciccarese S., and Massari S. Organization, structure and evolution of 41 kb of genomic DNA spanning the D-J-C region of the sheep TRB locus. Mol Immunol 45 (2008) 493-509
7. Hiraiwa H., Uenishi H., Kiuchi S., Watanabe M., Takagaki Y., and Yasue H. Assignment of T cell receptor (TCR) alpha-chain gene (A), beta-chain gene (B), gamma-chain gene (G), and delta-chain gene (D) loci on swine chromosomes by in situ hybridization and radiation hybrid mapping. Cytogenet Cell Genet 93 (2001) 94-99
8. Baron C., Sachs D.H., and LeGuern C. A particular TCR β variable region used by T cells infiltrating kidney transplants. J Immunol 166 (2001) 2589-2596
9. Butler J.E., Wertz N., Sun J., and Sacco R.E. Comparison of the expressed porcine Vβ and Jβ repertoire of thymocytes and peripheral T cells. Immunology 114 (2005) 184-193
10. Watanabe M., Iwasaki Y., Mita Y., Ota S., Yamada S., Shimizu M., et al. Porcine T-cell receptor β-chain: a genomic sequence covering Dβ1.1 to Cβ2 gene segments and the diversity of cDNA expressed in piglets including novel alternative splicing products. Mol Immunol 44 (2007) 2332-2343
11. Suzuki K., Asakawa S., Iida M., Shimanuki S., Fujishima N., Hiraiwa H., et al. Construction and evaluation of a porcine bacterial artificial chromosome library. Anim Genet 31 (2000) 8-12
12. Tanaka M., Suzuki K., Morozumi T., Kobayashi E., Matsumoto T., Domukai M., et al. Genomic structure and gene order of swine chromosome 7q1.1 → q1.2. Anim Genet 37 (2006) 10-16
13. Eguchi-Ogawa T., Morozumi T., Tanaka M., Shinkai H., Okumura N., Suzuki K., et al. Analysis of the genomic structure of the porcine CD1 gene cluster. Genomics 89 (2007) 248-261
14. Ewing B., and Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8 (1998) 186-194
15. Ewing B., Hillier L., Wendl M.C., and Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8 (1998) 175-185
16. Gordon D., Abajian C., and Green P. Consed: a graphical tool for sequence finishing. Genome Res 8 (1998) 195-202
17. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J Mol Biol 215 (1990) 403-410
18. Schwartz S., Zhang Z., Frazer K.A., Smit A., Riemer C., Bouck J., et al. PipMaker-a web server for aligning two genomic DNA sequences. Genome Res 10 (2000) 577-586
19. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16 (2000) 418-420
20. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 (1997) 4876-4882
21. Glusman G., Rowen L., Lee I., Boysen C., Roach J.C., Smit A.F., et al. Comparative genomics of the human and mouse T cell receptor loci. Immunity 15 (2001) 337-349
22. Shigeta A., Sato M., Kawashima T., Horiuchi H., Matsuda H., and Furusawa S. Genomic organization of the chicken T-cell receptor β chain D-J-C region. J Vet Med Sci 66 (2004) 1509-1515
23. Hardison R. Hemoglobins from bacteria to man: evolution of different patterns of gene expression. J Exp Biol 201 (1998) 1099-1117
24. Hunkapiller T., and Hood L. Diversity of the immunoglobulin gene superfamily. Adv Immunol 44 (1989) 1-63
25. Bahk Y.Y., Kappel C.A., Rasmussen G., and Kim B.S. Association between susceptibility to Theiler's virus-induced demyelination and T-cell receptor Jβ1-Cβ1 polymorphism rather than Vβ deletion. J Virol 71 (1997) 4181-4185
26. + natural killer T cells by α-galactosylceramide results in development of Th1 response and local host resistance in mice infected with Cryptococcus neoformans. Infect Immun 69 (2001) 213-220
27. + natural killer T cells by α-galactosylceramide in interleukin-18-deficient mice with systemic cryptococcosis. Infect Immun 69 (2001) 6643-6650
28. Toura I., Kawano T., Akutsu Y., Nakayama T., Ochiai T., and Taniguchi M. Cutting edge: inhibition of experimental tumor metastasis by dendritic cells pulsed with α-galactosylceramide. J Immunol 163 (1999) 2387-2391
29. Brigl M., van den Elzen P., Chen X., Meyers J.H., Wu D., Wong C.H., et al. Conserved and heterogeneous lipid antigen specificities of CD1d-restricted NKT cell receptors. J Immunol 176 (2006) 3625-3634
30. Van Rhijn I., Koets A.P., Im J.S., Piebes D., Reddington F., Besra G.S., et al. The bovine CD1 family contains group 1 CD1 proteins, but no functional CD1d. J Immunol 176 (2006) 4888-4893
31. Lunney J.K. Advances in swine biomedical model genomics. Int J Biol Sci 3 (2007) 179-184
32. Uenishi H., Hiraiwa H., Yamamoto R., Yasue H., Takagaki Y., Shiina T., et al. Genomic structure around joining segments and constant regions of swine T-cell receptor α/δ (TRA/TRD) locus. Immunology 109 (2003) 515-526
33. Uenishi H., Eguchi-Ogawa T., Toki D., Morozumi T., Tanaka-Matsuda M., Shinkai H., et al. Genomic sequence encoding diversity segments of the pig TCR δ chain gene demonstrates productivity of highly diversified repertoire. Mol Immunol 46 (2009) 1212-1221
34. Haas W., Pereira P., and Tonegawa S. γ/δ cells. Annu Rev Immunol 11 (1993) 637-685
35. Hein W.R., and Mackay C.R. Prominence of γδ T cells in the ruminant immune system. Immunol Today 12 (1991) 30-34
36. Uenishi H., Eguchi-Ogawa T., Shinkai H., Okumura N., Suzuki K., Toki D., et al. PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. Nucleic Acids Res 35 (2007) D650-D653