A complete DNA sequence map of the ovine Major Histocompatibility Complex

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Gao, Jianfeng ^a,b   Liu, Ka ^b,d   Liu, Haibo ^b,d   Blair, Hugh T ^c   Li, Gang ^a,b   Chen, Chuangfu ^a   Tan, Pingping ^b   Ma, Runlin Z ^b,d  

^a SHIHEZI UNIVERSITY   (China)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^c MASSEY UNIVERSITY   (New Zealand)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 3; MICRORNA;

ARTICLE; AUTOSOME; CATTLE; CHROMOSOME INVERSION; CONTROLLED STUDY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; SEQUENCE ANALYSIS; SHEEP; SPECIES DIFFERENCE; ANIMAL; BACTERIAL ARTIFICIAL CHROMOSOME; GENETICS; MOLECULAR GENETICS;

ANIMALIA; BOS; BOVINAE; MAMMALIA; OVIS; OVIS ARIES; SUIDAE;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; MAJOR HISTOCOMPATIBILITY COMPLEX; MICRORNAS; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SHEEP, DOMESTIC;

EID: 77955297231     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-466     Document Type: Article

References (50)

1. Danchin E, Vitiello V, Vienne A, Richard O, Gouret P, McDermott MF, Pontarotti P. The major histocompatibility complex origin. Immunological reviews 2004, 198:216-232. 10.1111/j.0105-2896.2004.00132.x, 15199965.
2. Flajnik MF, Kasahara M. Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. Immunity 2001, 15(3):351-362. 10.1016/S1074-7613(01)00198-4, 11567626.
3. Kaufman J. The origins of the adaptive immune system: whatever next?. Nature immunology 2002, 3(12):1124-1125. 10.1038/ni1202-1124, 12447367.
4. Escayg AP, Hickford JG, Bullock DW. Association between alleles of the ovine major histocompatibility complex and resistance to footrot. Research in veterinary science 1997, 63(3):283-287. 10.1016/S0034-5288(97)90035-7, 9491458.
5. Buitkamp J, Filmether P, Stear MJ, Epplen JT. Class I and class II major histocompatibility complex alleles are associated with faecal egg counts following natural, predominantly Ostertagia circumcincta infection. Parasitology research 1996, 82(8):693-696. 10.1007/s004360050187, 8897503.
6. Konnai S, Takeshima SN, Tajima S, Yin SA, Okada K, Onuma M, Aida Y. The influence of ovine MHC class II DRB1 alleles on immune response in bovine leukemia virus infection. Microbiology and immunology 2003, 47(3):223-232.
7. The MHC Sequencing Consortium Complete sequence and gene map of a human major histocompatibility complex. Nature 1999, 401(6756):921-923. 10.1038/44853, 10553908, The MHC Sequencing Consortium.
8. Takada T, Kumanovics A, Amadou C, Yoshino M, Jones EP, Athanasiou M, Evans GA, Fischer Lindahl K. Species-specific class I gene expansions formed the telomeric 1 mb of the mouse major histocompatibility complex. Genome research 2003, 13(4):589-600. 10.1101/gr.975303, 430170, 12671000.
9. Xie T, Rowen L, Aguado B, Ahearn ME, Madan A, Qin S, Campbell RD, Hood L. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome research 2003, 13(12):2621-2636. 10.1101/gr.1736803, 403804, 14656967.
10. Hurt P, Walter L, Sudbrak R, Klages S, Muller I, Shiina T, Inoko H, Lehrach H, Gunther E, Reinhardt R, Himmelbauer H. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Genome research 2004, 14(4):631-639. 10.1101/gr.1987704, 383307, 15060004.
11. Debenham SL, Hart EA, Ashurst JL, Howe KL, Quail MA, Ollier WE, Binns MM. Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species. Genomics 2005, 85(1):48-59. 10.1016/j.ygeno.2004.09.009, 15607421.
12. Yuhki N, Beck T, Stephens RM, Nishigaki Y, Newmann K, O'Brien SJ. Comparative genome organization of human, murine, and feline MHC class II region. Genome research 2003, 13(6A):1169-1179. 10.1101/gr.976103, 403645, 12743023.
13. Renard C, Hart E, Sehra H, Beasley H, Coggill P, Howe K, Harrow J, Gilbert J, Sims S, Rogers J, Ando A, Shigenari A, Shiina T, Inoko H, Chardon P, Beck S. The genomic sequence and analysis of the swine major histocompatibility complex. Genomics 2006, 88(1):96-110. 10.1016/j.ygeno.2006.01.004, 16515853.
14. Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JG, Benos PV, Samollow PB, Speed TP, Graves JA, Miller RD. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biology 2006, 4(3):e46. 10.1371/journal.pbio.0040046, 1351924,1351924, 16435885.
15. Matsuo MY, Asakawa S, Shimizu N, Kimura H, Nonaka M. Nucleotide sequence of the MHC class I genomic region of a teleost, the medaka (Oryzias latipes). Immunogenetics 2002, 53(10-11):930-940. 10.1007/s00251-001-0427-3, 11862394.
16. Ohta Y, Okamura K, McKinney EC, Bartl S, Hashimoto K, Flajnik MF. Primitive synteny of vertebrate major histocompatibility complex class I and class II genes. Proceedings of the National Academy of Sciences of the United States of America 2000, 97(9):4712-4717. 10.1073/pnas.97.9.4712, 18298, 10781076.
17. Terado T, Okamura K, Ohta Y, Shin DH, Smith SL, Hashimoto K, Takemoto T, Nonaka MI, Kimura H, Flajnik MF, Nonaka M. Molecular cloning of C4 gene and identification of the class III complement region in the shark MHC. J Immunol 2003, 171(5):2461-2466.
18. Shiina T, Shimizu S, Hosomichi K, Kohara S, Watanabe S, Hanzawa K, Beck S, Kulski JK, Inoko H. Comparative genomic analysis of two avian (quail and chicken) MHC regions. J Immunol 2004, 172(11):6751-6763.
19. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Camara F, Ermolaeva O, Henrichsen CN, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, NY) 2009, 324(5926):522-528.
20. Bonneaud C, Richard M, Faivre B, Westerdahl H, Sorci G. An Mhc class I allele associated to the expression of T-dependent immune response in the house sparrow. Immunogenetics 2005, 57(10):782-789. 10.1007/s00251-005-0046-5, 16189664.
21. Dukkipati VS, Blair HT, Garrick DJ, Murray A. 'Ovar-Mhc' - ovine major histocompatibility complex: structure and gene polymorphisms. Genet Mol Res 2006, 5(4):581-608.
22. Galindo RC, Ayoubi P, Garcia-Perez AL, Naranjo V, Kocan KM, Gortazar C, de la Fuente J. Differential expression of inflammatory and immune response genes in sheep infected with Anaplasma phagocytophilum. Veterinary immunology and immunopathology 2008, 126(1-2):27-34. 10.1016/j.vetimm.2008.06.004, 18640728.
23. Mena A, Nichani AK, Popowych Y, Godson DL, Dent D, Townsend HG, Mutwiri GK, Hecker R, Babiuk LA, Griebel P. Innate immune responses induced by CpG oligodeoxyribonucleotide stimulation of ovine blood mononuclear cells. Immunology 2003, 110(2):250-257. 10.1046/j.1365-2567.2003.01722.x, 1783041, 14511239.
24. Gruszczynska J, Brokowska K, Charon KM, Swiderek WP. Restriction fragment length polymorphism of exon 2 Ovar-DRB1 gene in Polish Heath Sheep and Polish Lowland Sheep. Journal of applied genetics 2005, 46(3):311-314.
25. Miltiadou D, Ballingall KT, Ellis SA, Russell GC, McKeever DJ. Haplotype characterization of transcribed ovine major histocompatibility complex (MHC) class I genes. Immunogenetics 2005, 57(7):499-509. 10.1007/s00251-005-0008-y, 16028041.
26. Liu H, Liu K, Wang J, Ma RZ. A BAC clone-based physical map of ovine major histocompatibility complex. Genomics 2006, 88(1):88-95. 10.1016/j.ygeno.2006.02.006, 16595171.
27. Deverson EV, Wright H, Watson S, Ballingall K, Huskisson N, Diamond AG, Howard JC. Class II major histocompatibility complex genes of the sheep. Animal genetics 1991, 22(3):211-225. 10.1111/j.1365-2052.1991.tb00671.x, 1928827.
28. Ballingall KT, Fardoe K, McKeever DJ. Genomic organisation and allelic diversity within coding and non-coding regions of the Ovar-DRB1 locus. Immunogenetics 2008, 60(2):95-103. 10.1007/s00251-008-0278-2, 18253728.
29. Scott PC, Choi CL, Brandon MR. Genetic organization of the ovine MHC class II region. Immunogenetics 1987, 25(2):116-122. 10.1007/BF00364277, 3028945.
30. Escayg AP, Hickford JG, Montgomery GW, Dodds KG, Bullock DW. Polymorphism at the ovine major histocompatibility complex class II loci. Animal genetics 1996, 27(5):305-312. 10.1111/j.1365-2052.1996.tb00974.x, 8930070.
31. Snibson KJ, Maddox JF, Fabb SA, Brandon MR. Allelic variation of ovine MHC class II DQA1 and DQA2 genes. Animal genetics 1998, 29(5):356-362. 10.1046/j.1365-2052.1998.295351.x, 9800324.
32. van der Poel JJ, Groenen MA, Dijkhof RJ, Ruyter D, Giphart MJ. The nucleotide sequence of the bovine MHC class II alpha genes: DRA, DOA, and DYA. Immunogenetics 1990, 31(1):29-36. 10.1007/BF00702486, 2298463.
33. McShane RD, Gallagher DS, Newkirk H, Taylor JF, Burzlaff JD, Davis SK, Skow LC. Physical localization and order of genes in the class I region of the bovine MHC. Animal genetics 2001, 32(5):235-239. 10.1046/j.1365-2052.2001.00758.x, 11683708.
34. Amills M, Ramiya V, Norimine J, Lewin HA. The major histocompatibility complex of ruminants. Revue scientifique et technique (International Office of Epizootics) 1998, 17(1):108-120.
35. Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarajan S, Goldammer T, Lee JH, McKay S, Womack JE, Lewin HA. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome research 2004, 14(7):1424-1437. 10.1101/gr.2554404, 442159, 15231756.
36. Childers CP, Newkirk HL, Honeycutt DA, Ramlachan N, Muzney DM, Sodergren E, Gibbs RA, Weinstock GM, Womack JE, Skow LC. Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes. Animal genetics 2006, 37(2):121-129. 10.1111/j.1365-2052.2005.01395.x, 16573526.
37. Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, Cribiu EP, Freking BA, Beh KJ, Cockett NE, Kang N, Riffkin CD, Drinkwater R, Moore SS, Dodds KG, Lumsden JM, van Stijn TC, Phua SH, Adelson DL, Burkin HR, Broom JE, Buitkamp J, Cambridge L, Cushwa WT, Gerard E, Galloway SM, Harrison B, Hawken RJ, Hiendleder S, Henry HM, Medrano JF, et al. An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome research 2001, 11(7):1275-1289. 10.1101/gr.GR-1350R, 311104, 11435411.
38. Liu K, Zhang P, GaO J, Liu H, Li G, Qiu Z, Zhang Y, Ren J, Tan P, Ma RZ. Closing a gap in the physical map of the ovine major histocompatibility complex. Animmal Genetics
39. Qin J, Mamotte C, Cockett NE, Wetherall JD, Groth DM. A map of the class III region of the sheep major histocompatibilty complex. BMC genomics 2008, 9:409. 10.1186/1471-2164-9-409, 2566321, 18786271.
40. Herrmann-Hoesing LM, White SN, Kappmeyer LS, Herndon DR, Knowles DP. Genomic analysis of Ovis aries (Ovar) MHC class IIa loci. Immunogenetics 2008, 60(3-4):167-176. 10.1007/s00251-008-0275-5, 18322680.
41. Glass EJ, Oliver RA, Russell GC. Duplicated DQ haplotypes increase the complexity of restriction element usage in cattle. J Immunol 2000, 165(1):134-138.
42. Skow LC, Snaples SN, Davis SK, Taylor JF, Huang B, Gallagher DH. Localization of bovine lymphocyte antigen (BoLA) DYA and class I loci to different regions of chromosome 23. Mamm Genome 1996, 7(5):388-389. 10.1007/s003359900112, 8661732.
43. Band M, Larson JH, Womack JE, Lewin HA. A radiation hybrid map of BTA23: identification of a chromosomal rearrangement leading to separation of the cattle MHC class II subregions. Genomics 1998, 53(3):269-275. 10.1006/geno.1998.5507, 9799592.
44. Andersson L, Rask L. Characterization of the MHC class II region in cattle. The number of DQ genes varies between haplotypes. Immunogenetics 1988, 27(2):110-120. 10.1007/BF00351084, 2891610.
45. Itoh T, Watanabe T, Ihara N, Mariani P, Beattie CW, Sugimoto Y, Takasuga A. A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics 2005, 85(4):413-424. 10.1016/j.ygeno.2004.12.007, 15780744.
46. Ogg SL, Weldon AK, Dobbie L, Smith AJ, Mather IH. Expression of butyrophilin (Btn1a1) in lactating mammary gland is essential for the regulated secretion of milk-lipid droplets. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(27):10084-10089. 10.1073/pnas.0402930101, 454168, 15226505.
47. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, et al. The genome sequence of Drosophila melanogaster. Science (New York, NY) 2000, 287(5461):2185-2195.
48. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of molecular biology 1990, 215(3):403-410.
49. Potter SC, Clarke L, Curwen V, Keenan S, Mongin E, Searle SM, Stabenau A, Storey R, Clamp M. The Ensembl analysis pipeline. Genome research 2004, 14(5):934-941. 10.1101/gr.1859804, 479123, 15123589.
50. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 1999, 27(2):573-580. 10.1093/nar/27.2.573, 148217, 9862982.