Analysis of the genomic structure of the porcine CD1 gene cluster

Genomics

Volumn 89, Issue 2, 2007, Pages 248-261

  Eguchi Ogawa, Tomoko ^a   Morozumi, Takeya ^a,b   Tanaka, Maiko ^a,b   Shinkai, Hiroki ^a,b   Okumura, Naohiko ^a,b   Suzuki, Kohei ^a,b   Awata, Takashi ^a   Uenishi, Hirohide ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b Second Research Division   (Japan)

Author keywords

CD1; Immunogenetics; Molecular evolution; Sus scrofa

Indexed keywords

ANTIGEN; CD1 ANTIGEN; LIPID; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; T LYMPHOCYTE RECEPTOR;

ANIMAL TISSUE; ANTIGEN PRESENTATION; ARTICLE; CD1 GENE; CONTROLLED STUDY; DNA SEQUENCE; GENE; GENE CLUSTER; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; KIRREL GENE; MAMMALIAN GENETICS; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OLFACTORY RECEPTOR; OR GENE; PRIORITY JOURNAL; PROTEIN FUNCTION; RAT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURAL GENOMICS; SWINE;

ANIMALS; ANTIGENS, CD1; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA PRIMERS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION; GENOME; HUMANS; IMMUNOGENETICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; RECEPTORS, ODORANT; SUS SCROFA;

MAMMALIA; SUIDAE; SUS SCROFA;

EID: 33846017345     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2006.10.003     Document Type: Article

References (51)

1. Germain R.N., and Margulies D.H. The biochemistry and cell biology of antigen processing and presentation. Annu. Rev. Immunol. 11 (1993) 403-450
2. Porcelli S.A., and Modlin R.L. The CD1 system: antigen-presenting molecules for T cell recognition of lipids and glycolipids. Annu. Rev. Immunol. 17 (1999) 297-329
3. Park S.H., and Bendelac A. CD1-restricted T-cell responses and microbial infection. Nature 406 (2000) 788-792
4. Brigl M., and Brenner M.B. CD1: antigen presentation and T cell function. Annu. Rev. Immunol. 22 (2004) 817-890
5. + T cells. Nature 372 (1994) 691-694
6. Moody D.B., et al. Structural requirements for glycolipid antigen recognition by CD1b-restricted T cells. Science 278 (1997) 283-286
7. Moody D.B., et al. T cell activation by lipopeptide antigens. Science 303 (2004) 527-531
8. Sieling P.A., et al. CD1-restricted T cell recognition of microbial lipoglycan antigens. Science 269 (1995) 227-230
9. Gumperz J.E., et al. Murine CD1d-restricted T cell recognition of cellular lipids. Immunity 12 (2000) 211-221
10. Kawano T., et al. CD1d-restricted and TCR-mediated activation of Vα14 NKT cells by glycosylceramides. Science 278 (1997) 1626-1629
11. Bradbury A., Belt K.T., Neri T.M., Milstein C., and Calabi F. Mouse CD1 is distinct from and co-exists with TL in the same thymus. EMBO J. 7 (1988) 3081-3086
12. Chun T., Wang K., Zuckermann F.A., and Gaskins H.R. Molecular cloning and characterization of a novel CD1 gene from the pig. J. Immunol. 162 (1999) 6562-6571
13. Dascher C.C., et al. Conservation of a CD1 multigene family in the guinea pig. J. Immunol. 163 (1999) 5478-5488
14. Ferguson E.D., Dutia B.M., Hein W.R., and Hopkins J. The sheep CD1 gene family contains at least four CD1B homologues. Immunogenetics 44 (1996) 86-96
15. Hayes S.M., and Knight K.L. Group 1 CD1 genes in rabbit. J. Immunol. 166 (2001) 403-410
16. Ichimiya S., Kikuchi K., and Matsuura A. Structural analysis of the rat homologue of CD1: evidence for evolutionary conservation of the CD1D class and widespread transcription by rat cells. J. Immunol. 153 (1994) 1112-1123
17. Shiina T., et al. Genomic anatomy of a premier major histocompatibility complex paralogous region on chromosome 1q21-q22. Genome Res. 11 (2001) 789-802
18. Miller M.M., et al. Characterization of two avian MHC-like genes reveals an ancient origin of the CD1 family. Proc. Natl. Acad. Sci. USA 102 (2005) 8674-8679
19. Salomonsen J., et al. Two CD1 genes map to the chicken MHC, indicating that CD1 genes are ancient and likely to have been present in the primordial MHC. Proc. Natl. Acad. Sci. USA 102 (2005) 8668-8673
20. Maruoka T., Tanabe H., Chiba M., and Kasahara M. Chicken CD1 genes are located in the MHC: CD1 and endothelial protein C receptor genes constitute a distinct subfamily of class-I-like genes that predates the emergence of mammals. Immunogenetics 57 (2005) 590-600
21. Pennisi E. Evolution: chimp genome draft online. Science 302 (2003) 1876
22. Oakey R.J., Watson M.L., and Seldin M.F. Construction of a physical map on mouse and human chromosome 1: comparison of 13 Mb of mouse and 11 Mb of human DNA. Hum. Mol. Genet. 1 (1992) 613-620
23. Uenishi H., et al. PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. Nucleic Acids Res. 32 (2004) D484-D488
24. McCullough K.C., Schaffner R., Natale V., Kim Y.B., and Summerfield A. Phenotype of porcine monocytic cells: modulation of surface molecule expression upon monocyte differentiation into macrophages. Vet. Immunol. Immunopathol. 58 (1997) 265-275
25. Lefranc M.P., et al. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev. Comp. Immunol. 29 (2005) 185-203
26. Bradbury A., Milstein C., and Kozak C.A. Chromosomal localization of Cd1d genes in the mouse. Somatic Cell Mol. Genet. 17 (1991) 93-96
27. Renard C., Chardon P., and Vaiman M. The phylogenetic history of the MHC class I gene families in pig, including a fossil gene predating mammalian radiation. J. Mol. Evol. 57 (2003) 420-434
28. Shinkai H., et al. Genomic structure of eight porcine chemokine receptors and intergene sharing of an exon between CCR1 and XCR1. Gene 349 (2005) 55-66
29. Uenishi H., 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
30. Li W.H., Gojobori T., and Nei M. Pseudogenes as a paradigm of neutral evolution. Nature 292 (1981) 237-239
31. Kumar S., and Hedges S.B. A molecular timescale for vertebrate evolution. Nature 392 (1998) 917-920
32. Lefranc M.P., et al. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MHCSF) G-LIKE-DOMAIN. Dev. Comp. Immunol. 29 (2005) 917-938
33. Dascher C.C., and Brenner M.B. Evolutionary constraints on CD1 structure: insights from comparative genomic analysis. Trends Immunol. 24 (2003) 412-418
34. Kulski J.K., Dunn D.S., Gaudieri S., Shiina T., and Inoko H. Genomic and phylogenetic analysis of the human CD1 and HLA class I multicopy genes. J. Mol. Evol. 53 (2001) 642-650
35. Calabi F., and Bradbury A. The CD1 system. Tissue Antigens 37 (1991) 1-9
36. Moody D.B., and Porcelli S.A. Intracellular pathways of CD1 antigen presentation. Nat. Rev. Immunol. 3 (2003) 11-22
37. Ohta T. Effect of gene conversion on polymorphic patterns at major histocompatibility complex loci. Immunol. Rev. 167 (1999) 319-325
38. Zeng Z., et al. Crystal structure of mouse CD1: an MHC-like fold with a large hydrophobic binding groove. Science 277 (1997) 339-345
39. Yamamoto R., et al. Jα-gene segment usage and the CDR3 diversity of porcine TCRα-chain cDNA clones from the PBL of a five-month-old pig and the thymus of a one-month-old pig. Mol. Immunol. 42 (2005) 1375-1383
40. Holtmeier W., et al. Development and compartmentalization of the porcine TCR δ repertoire at mucosal and extraintestinal sites: the pig as a model for analyzing the effects of age and microbial factors. J. Immunol. 169 (2002) 1993-2002
41. Yamamoto R., et al. TRAV gene usage in pig T-cell receptor α cDNA. Immunogenetics 57 (2005) 219-225
42. Yang Y.G., Ohta S., Yamada S., Shimizu M., and Takagaki Y. Diversity of T cell receptor δ-chain cDNA in the thymus of a one-month-old pig. J. Immunol. 155 (1995) 1981-1993
43. Tanaka M., et al. Genomic structure and gene order of the region on swine chromosome 7q1.1 → q1.2. Anim. Genet. 37 (2005) 10-16
44. Suzuki K., et al. Construction and evaluation of a porcine bacterial artificial chromosome library. Anim. Genet. 31 (2000) 8-12
45. Gordon D., Abajian C., and Green P. Consed: a graphical tool for sequence finishing. Genome Res. 8 (1998) 195-202
46. Schwartz S., et al. PipMaker-A web server for aligning two genomic DNA sequences. Genome Res. 10 (2000) 577-586
47. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
48. Paillot R., Laval F., Audonnet J.C., Andreoni C., and Juillard V. Functional and phenotypic characterization of distinct porcine dendritic cells derived from peripheral blood monocytes. Immunology 102 (2001) 396-404
49. Saalmuller A., et al. Summary of the animal homologue section of HLDA8. Cell. Immunol. 236 (2005) 51-58
50. Shimamura M., Abe H., Nikaido M., Ohshima K., and Okada N. Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. Mol. Biol. Evol. 16 (1999) 1046-1060
51. Lefranc M.P., et al. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 33 (2005) D593-D597