Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat

PLoS ONE

Volumn 3, Issue 7, 2008, Pages

  Yuhki, Naoya ^a   Mullikin, James C ^b   Beck, Thomas ^c   Stephens, Robert ^c   O'Brien, Stephen J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; HLA DP ANTIGEN; HLA DQ ANTIGEN; HLA DR ANTIGEN; HLA DRA ANTIGEN; HLA DRB ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 3; PROTEIN DMA; PROTEIN DMB; PROTEIN DOA; PROTEIN DOB; PROTEIN ECE1; PROTEIN FERVMLU1; PROTEIN FERVMLU2; PROTEIN FLAI A; PROTEIN FLAI E; PROTEIN FLAI H; PROTEIN FLAI K; PROTEIN FLAI S; PROTEIN LMP2; PROTEIN LMP7; PROTEIN TAPASIN; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 2; ANTIGEN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ANTIGEN PRESENTATION; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CAT; CHROMOSOME BREAKAGE; CHROMOSOME INVERSION; CONTROLLED STUDY; DOMESTIC ANIMAL; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC CODE; GENETIC CONSERVATION; GENOME; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; OLFACTORY RECEPTOR; PROTEIN STRUCTURE; PSEUDOGENE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; CHEMISTRY; CHROMOSOME; ENDOGENOUS RETROVIRUS; GENETICS; HAPLOTYPE; HOMOZYGOTE; METABOLISM; NUCLEOTIDE REPEAT; ULTRASTRUCTURE;

FELIDAE; FELIS CATUS; PAPIO;

ANIMALS; ANTIGENS; CATS; CHROMOSOMES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; ENDOGENOUS RETROVIRUSES; HAPLOTYPES; HOMOZYGOTE; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; OLFACTORY RECEPTOR NEURONS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, ODORANT; REPETITIVE SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

EID: 50549088884     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002674     Document Type: Article

References (46)

1. Klein J (1986) Natural history of the major histocompatibility complex. New York: John Wiley and Sons.
2. Younger RM, Amadou C, Bethel G, Ehlers A, Fischer Lindahl K, et al. (2001) Characterization of Clustered MHC-Linked Olfactory Receptor Genes in Human and Mouse. Genome Res 11(4): 519-530.
3. Loconto J, Papes F, Chang E, Stowers L, Jones EP, et al. (2003) Functional expression of murine V2R pheromone receptors involves selective association with the M10 and M1 families of MHC class Ib molecules. Cell 112(5): 6-8-612.
4. Okita K, Ichisaka T, Yamanaka S (2007) Generation of germline-competent induced pluripotent stem cells. Nature 448(7151): 313-317.
5. The MHC Sequencing Consortium (1999) Complete sequence and gene map of a human major histocompatibility complex. Nature 401: 921-923.
6. Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, et al. (2008) Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project. Immunogenet 60: 1-18.
7. Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles, et al. (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet 2: e9.
8. Horton R, Wilming LRV, Lovering RC, Bruford EA, Khodiyar VK, et al. (2004) Gene map of the extended human MHC. Nat Rev Genet 5: 889-899.
9. Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, et al. (2004) Complete MHC haplotype sequencing for common disease gene mapping. Gen Res 14: 1176-1187.
10. Allcock RJ, Atrazhev AM, Beck S, de Jong PJ, Elliott JF, et al. (2002) The MHC haplotype project: a resource for HLA-linked association studies. Tissue Antigens 59: 520-521.
11. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
12. Hardy WD, Essex M, McClelland A (1980) Feline Leukemia Virus. New York: Elsevier Publishers.
13. Brown EW, Yuhki N, Packer C, O'Brien SJ (1994) A lion lentivirus related to feline immunodeficiency virus: epidemiologic and phylogenetic aspects. J Virol 68(9): 5953-5968.
14. Carpenter MA, Brown EW, Culver M, Johnson WE, Pecon-Slattery J, et al. (1996) Genetic and phylogenetic divergence of feline immunodeficiency virus in the puma (Puma concolor). J Virol 70(10): 6682-6693.
15. Troyer JL, Pecon-Slattery J, Roelke ME, Black L, Packer C, et al. (2004) Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free-ranging population of African lions. J Virol 78(7): 3777-3791.
16. Troyer JL, Pecon-Slattery J, Roelke ME, Johnson W, VandeWoude S, et al. (2005) Seroprevalence and genomic divergence of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species. J Virol 79(13): 8282-8294.
17. Pearks Wilkerson AJ, Teeling EC, Troyer JL, Bar-Gal GK, Roelke M, et al. (2004) Coronavirus outbreak in cheetahs: lessons for SARS. Curr Biol 14(6): R227-228.
18. Yuhki N, Beck T, Stephens RM, Nishigaki Y, Newmann Y, et al. (2003) Comparative genome organization of human, murine and feline major histocompatibility complex class II region. Genome Res 13: 1169-1179.
19. Beck T, Menninger J, Murphy WJ, Nash WG, O'Brien SJ, et al. (2005) The feline major histocompatibility complex is rearranged by inversion with a breakpoint in the distal class I region. Immunogenet 56: 702-709.
20. Yuhki N, Beck T, Stephens R, Neelam B, O'Brien SJ (2007) Comparative genomic structure of human, dog, and cat MHC: HLA DLA, and FLA. J Hered 98(5): 390-399.
21. Beck TW, Menninger J, Voight G, Newmann K, Nishigaki Y, et al. (2001) Comparative feline genomics: A BAC/PAC contig map of the major histocompatibility complex class II region. Genomics 71: 282-295.
22. Ewing B, Green P (1998a) Base calling of automated sequencer traces using phred II error probabilities. Gen Res 8: 186-194.
23. Ewing B, Hillier L, Wendi M, Green P (1998) Basecalling of automated sequencer traces using phred I accuracy assessment. Gen Res 8: 175-185.
24. Gordon D, Desmarais C, Green P (2001) Automated finishing with Autofinish. Gen Res 11: 614-625.
25. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
26. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 268: 78-94.
28. Yuhki N, Heidecker GF, O'Brien SJ (1989) Characterization of major histocompatibility complex cDNA clones in the domestic cat: Diversity and evolution of MHC class I genes. J Immunol 142: 3676-3682.
29. Tatusova TA, Madden TL (1999) Blast 2 sequences - a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247-250.
30. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, et al. (2000) PipMaker - A web server for aligning two genomic DNA sequences. Gen Res 10(4): 577-586.
31. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-mouse alignments with BLASTZ. Gen Res 13: 103-107.
32. Pontius J, Mullikin JC, Smith D, Lindblad-Toh K, Gnerre S, et al. (2007) The domestic cat genome sequence: Annotation and comparative inferences. Genome Res: Submitted.
33. Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM, et al. (2000) An SNP map of human chromosome 22. Nature 407(6803): 516-520.
34. Wheelan SJ, Church DM, Ostell JM (2001) Spidey: a tool for mRNA-to-genomic alignments. Gen Res 11: 1952-1957.
35. Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Gen Res 14: 988-995.
36. Yuhki N, O'Brien SJ (1997) Nature and origin of polymorphism in feline MHC class II DRA and DRB genes. J Immunol 158: 2822-2833.
37. Krawczyk M, Peyraud N, Rybtsova N, Masternak K, Bucher P, et al. (2004) Long distance control of MHC class II expression by multiple distal enhancers regulated by regulatory factor X complex and CIITA. J Immunol 173: 6200-6210.
38. van den Elsen PJ, obin SJP, van Eggermond MCAJ, Peijnenburg A (1998) Regulation of MHC class I and class II gene transcription: differences and similarities. Immunogenet 48: 208-221.
39. Koller BH, Geraghty DE, Shimizu Y, DeMars R, Orr HT (1988) HLA-E, A novel HLA class I gene expressed in resting T lymphocytes. J Immunol 141(3): 897-904.
40. Takahashi K, Rooney AP, Nei M (2000) Origins and divergence times of mammalian class II MHC gene clusters. J Hered 91(3): 198-204.
41. Yuhki N, O'Brien SJ (1990) DNA recombination and natural selection pressure sustain genetic sequence diversity of the feline MHC class I genes. J Exp Med 172(2): 621-630.
42. Roca AL, Pecon-Slattery J, O'Brien SJ (2004) Intact endogenous feline leukemia viruses of recent origin. J Virol 78(8): 4370-4375.
43. Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ (2005) Insertional polymorphisms of endogenous feline leukemia viruses. J Virol 79(7): 3979-3986.
44. Klement V, McAllister RM (1972) Syncytial cytopathic effect in KB cells of a C-type RNA virus isolated from human rhabdomyosarcoma. Virology 50: 305-308.
45. Nelson-Rees WA, Klement V, Peterson WD Jr, Weaver JF (1973) Comparative study of two RD 114 virus-indicator cell lines, KC and KB. J Natl. Cancer Inst 50: 1129-1135.
46. Niman HL, Stephenson JR, Gardner MB, Roy-Burman P (1977) RD-114 and feline leukaemia virus genome expression in natural lymphomas of domestic cats. Nature (London) 266: 357-360.