MHC-linked and un-linked class I genes in the wallaby

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Siddle, Hannah V ^a   Deakin, Janine E ^c   Coggill, Penny ^b   Hart, Elizabeth ^b   Cheng, Yuanyuan ^a   Wong, Emily S W ^a   Harrow, Jennifer ^b   Beck, Stephan ^d   Belov, Katherine ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

ANTIGEN PRESENTATION; ARHGAP20 GENE; ARPP19 GENE; ARTICLE; CHROMOSOME 2Q; CONTROLLED STUDY; GENE; GENE LOCATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC LINKAGE; GENOME; GPR128 GENE; HNRPM GENE; MARSUPIAL; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RETROVIRUS; TATA BOX; WALLABY; ANIMAL; BACTERIAL ARTIFICIAL CHROMOSOME; DNA SEQUENCE; ENDOGENOUS RETROVIRUS; GENE EXPRESSION PROFILING; GENETIC POLYMORPHISM; GENETICS; MOLECULAR GENETICS; PROMOTER REGION; SPECIES DIFFERENCE;

EUTHERIA; MACROPUS EUGENII; MAMMALIA; METATHERIA; VERTEBRATA;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONSERVED SEQUENCE; ENDOGENOUS RETROVIRUSES; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENES, MHC CLASS I; LINKAGE (GENETICS); MACROPODIDAE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 68849086398     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-310     Document Type: Article

References (58)

1. Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 1987, 329:506-512. 10.1038/329506a0, 3309677.
2. Hughes A, Nei M. Pattern of nucleotide substitution at the major histocompatibility complex class I loci reveals overdominant selection. Nature 1988, 335:1670170.
3. Kelley J, Walter L, Trowsdale J. Comparative genomics of major histocompatibility complexes. Immunogenetics 2005, 56:683-695. 10.1007/s00251-004-0717-7, 15605248.
4. Otting N, Heijmans CM, Noort RC, de Groot NG, Doxiadis GG, van Rood JJ, Watkins DI, Bontrop RE. Unparalleled complexity of the MHC class I region in rhesus macaques. Proc Natl Acad Sci USA 2005, 102:1626-1631. 545086, 15665097, 10.1073/pnas.0409084102.
5. Kaufman J. Co-evolving genes in MHC haplotypes: the "rule" for nonmammalian vertebrates?. Immunogenetics 1999, 50:228-236. 10.1007/s002510050597, 10602883.
6. Flajnik MF, Kasahara M. Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. Immunity 2001, 15:351-362. 10.1016/S1074-7613(01)00198-4, 11567626.
7. 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, 172:6751-6763.
8. Stroynowski I, Lindahl KF. Antigen presentation by non-classical class I molecules. Curr Opin Immunol 1994, 6:38-44. 10.1016/0952-7915(94)90031-0, 8172679.
9. Braud VM, Allan DS, O'Callaghan CA, Soderstrom K, D'Andrea A, Ogg GS, Lazetic S, Young NT, Bell JI, Phillips JH, et al. HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C. Nature 1998, 391:795-799. 10.1038/35869, 9486650.
10. Lepin EJ, Bastin JM, Allan DS, Roncador G, Braud VM, Mason DY, Merwe PA, McMichael AJ, Bell JI, Powis SH, O'Callaghan CA. Functional characterization of HLA-F and binding of HLA-F tetramers to ILT2 and ILT4 receptors. Eur J Immunol 2000, 30:3552-3561. 10.1002/1521-4141(200012)30:12<3552::AID-IMMU3552>3.0.CO;2-L, 11169396.
11. Tripathi P, Naik S, Agrawal S. HLA-E and immunobiology of pregnancy. Tissue Antigens 2006, 67:207-213. 10.1111/j.1399-0039.2005.00550.x, 16573557.
12. Kovats S, Main EK, Librach C, Stubblebine M, Fisher SJ, DeMars R. A class I antigen, HLA-G, expressed in human trophoblasts. Science 1990, 248:220-223. 10.1126/science.2326636, 2326636.
13. Kumanovics A, Fischer Lindahl K. Good copy, bad copy: choosing animal models for HLA-linked diseases. Curr Opin Genet Dev 2004, 14:258-263. 10.1016/j.gde.2004.04.002, 15172668.
14. Moon DA, Veniamin SM, Parks-Dely JA, Magor KE. The MHC of the duck (Anas platyrhynchos) contains five differentially expressed class I genes. J Immunol 2005, 175:6702-6712.
15. Flajnik MF, Kasahara M, Shum BP, Salter-Cid L, Taylor E, Du Pasquier L. A novel type of class I gene organization in vertebrates: a large family of non-MHC-linked class I genes is expressed at the RNA level in the amphibian Xenopus. Embo J 1993, 12:4385-4396. 413735, 8223448.
16. Gouin N, Wright AM, Miska KB, Parra ZE, Samollow PB, Baker ML, Miller RD. Modo-UG, a marsupial nonclassical MHC class I locus. Immunogenetics 2006, 58:396-406. 10.1007/s00251-006-0115-4, 16738937.
17. Nei M, Gu X, Sitnikova T. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci USA 1997, 94:7799-7806. 33709, 9223266, 10.1073/pnas.94.15.7799.
18. Rogers JH. Mouse histocompatibility-related genes are not conserved in other mammals. Embo J 1985, 4:749-753. 554251, 4006905.
19. Adams EJ, Parham P. Species-specific evolution of MHC class I genes in the higher primates. Immunol Rev 2001, 183:41-64. 10.1034/j.1600-065x.2001.1830104.x, 11782246.
20. Kaufman J, Milne S, Gobel TW, Walker BA, Jacob JP, Auffray C, Zoorob R, Beck S. The chicken B locus is a minimal essential major histocompatibility complex. Nature 1999, 401:923-925. 10.1038/44856, 10553909.
21. Nonaka M, Namikawa C, Kato Y, Sasaki M, Salter-Cid L, Flajnik MF. Major histocompatibility complex gene mapping in the amphibian Xenopus implies a primordial organization. Proc Natl Acad Sci USA 1997, 94:5789-5791. 20858, 9159152, 10.1073/pnas.94.11.5789.
22. Ohta Y, McKinney EC, Criscitiello MF, Flajnik MF. Proteasome, transporter associated with antigen processing, and class I genes in the nurse shark Ginglymostoma cirratum: evidence for a stable class I region and MHC haplotype lineages. J Immunol 2002, 168:771-781.
23. Sambrook JG, Figueroa F, Beck S. A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish. BMC Genomics 2005, 6:152. 1309616, 16271140, 10.1186/1471-2164-6-152.
24. Kaufman J, Jacob J, Shaw I, Walker B, Milne S, Beck S, Salomonsen J. Gene organisation determines evolution of function in the chicken MHC. Immunol Rev 1999, 167:101-117. 10.1111/j.1600-065X.1999.tb01385.x, 10319254.
25. Ohta Y, Goetz W, Hossain MZ, Nonaka M, Flajnik MF. Ancestral organization of the MHC revealed in the amphibian Xenopus. J Immunol 2006, 176:3674-3685.
26. Sammut B, Du Pasquier L, Ducoroy P, Laurens V, Marcuz A, Tournefier A. Axolotl MHC architecture and polymorphism. Eur J Immunol 1999, 29:2897-2907. 10.1002/(SICI)1521-4141(199909)29:09<2897::AID-IMMU2897>3.0.CO;2-2 , 10508264.
27. Walter L, Tiemann C, Heine L, Gunther E. Genomic organization and sequence of the rat major histocompatibility complex class Ia gene RT1.Au. Immunogenetics 1995, 41:332. 10.1007/BF00172161, 7721358.
28. Briles WE, Goto RM, Auffray C, Miller MM. A polymorphic system related to but genetically independent of the chicken major histocompatibility complex. Immunogenetics 1993, 37:408-414. 10.1007/BF00222464, 8436415.
29. Jayawardena-Wolf J, Bendelac A. CD1 and lipid antigens: intracellular pathways for antigen presentation. Curr Opin Immunol 2001, 13:109-113. 10.1016/S0952-7915(00)00190-4, 11154926.
30. Joly E, Rouillon V. The orthology of HLA-E and H2-Qa1 is hidden by their concerted evolution with other MHC class I molecules. Biol Direct 2006, 1:2. 1403747, 16542007, 10.1186/1745-6150-1-2.
31. Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, et al. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol 2006, 4:e46. 1351924, 16435885, 10.1371/journal.pbio.0040046.
32. Deakin JE, Siddle HV, Cross JG, Belov K, Graves JA. Class I genes have split from the MHC in the tammar wallaby. Cytogenet Genome Res 2007, 116:205-211. 10.1159/000098188, 17317961.
33. Wakefield MJ, Graves JA. The kangaroo genome. Leaps and bounds in comparative genomics. EMBO Rep 2003, 4:143-147. 1315837, 12612602, 10.1038/sj.embor.embor739.
34. Nilsson MA, Gullberg A, Spotorno AE, Arnason U, Janke A. Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes. J Mol Evol 2003, 57(Suppl 1):S3-12. 10.1007/s00239-003-0001-8, 15008398.
35. Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI. Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 1990, 31:217-219.
36. Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, et al. Complete MHC haplotype sequencing for common disease gene mapping. Genome Res 2004, 14:1176-1187. 419796, 15140828, 10.1101/gr.2188104.
37. Siddle HV, Sanderson C, Belov K. Characterization of major histocompatibility complex class I and class II genes from the Tasmanian devil (Sarcophilus harrisii). Immunogenetics 2007, 59:753-60. 10.1007/s00251-007-0238-2, 17673996.
38. Lam MK, Belov K, Harrison GA, Cooper DW. An Mhc class I gene in the Australian brushtail possum (Trichosurus vulpecula). Immunogenetics 2001, 53:430-433. 10.1007/s002510100336, 11486282.
39. O'Neill RJ, O'Neill MJ, Graves JA. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 1998, 393:68-72. 10.1038/29985, 9590690.
40. Piontkivska H, Nei M. Birth-and-death evolution in primate MHC class I genes: divergence time estimates. Mol Biol Evol 2003, 20:601-609. 10.1093/molbev/msg064, 12679545.
41. Ferreri GC, Marzelli M, Rens W, O'Neill RJ. A centromere-specific retroviral element associated with breaks of synteny in macropodine marsupials. Cytogenet Genome Res 2004, 107:115-118. 10.1159/000079580, 15305065.
42. Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, Archidiacono N, Schwartz S, Rocchi M, Eichler EE. Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am J Hum Genet 2002, 70:83-100. 419985, 11731936, 10.1086/338458.
43. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008, 455:256.
44. Deakin JE, Koina E, Waters PD, Doherty R, Patel VS, Delbridge ML, Dobson B, Fong J, Hu Y, Hurk C, et al. Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals. Chromosome Res 2008, 16:1159-1175. 10.1007/s10577-008-1266-y, 18987984.
45. Rens W, O'Brien PC, Yang F, Solanky N, Perelman P, Graphodatsky AS, Ferguson MW, Svartman M, De Leo AA, Graves JA, Ferguson-Smith MA. Karyotype relationships between distantly related marsupials from South America and Australia. Chromosome Res 2001, 9:301-308. 10.1023/A:1016646629889, 11419794.
46. Kulski JK, Gaudieri S, Martin A, Dawkins RL. Coevolution of PERB11 (MIC) and HLA class I genes with HERV-16 and retroelements by extended genomic duplication. J Mol Evol 1999, 49:84-97. 10.1007/PL00006537, 10368437.
47. Joly E, Le Rolle AF, Gonzalez AL, Mehling B, Stevens J, Coadwell WJ, Hunig T, Howard JC, Butcher GW. Co-evolution of rat TAP transporters and MHC class I RT1-A molecules. Curr Biol 1998, 8:169-172. 10.1016/S0960-9822(98)70065-X, 9443915.
48. Amadou C. Evolution of the Mhc class I region: the framework hypothesis. Immunogenetics 1999, 49:362-367. 10.1007/s002510050507, 10079304.
49. Holland OJ, Cowan PE, Gleeson DM, Chamley LW. Identification of novel major histocompatibility complex class I sequences in a marsupial, the brushtail possum (Trichosurus vulpecula). Immunogenetics 2008, 60:609-619. 10.1007/s00251-008-0316-0, 18636252.
50. Hughes AL, Nei M. Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals. Mol Biol Evol 1989, 6:559-579.
51. Figueroa F, Gunther E, Klein J. MHC polymorphism pre-dating speciation. Nature 1988, 335:265-267. 10.1038/335265a0, 3137477.
52. Siddle HV, Deakin JE, Baker ML, Miller RD, Belov K. Isolation of major histocompatibility complex Class I genes from the tammar wallaby (Macropus eugenii). Immunogenetics 2006, 58:487-493. 10.1007/s00251-006-0107-4, 16568263.
53. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 308517, 7984417, 10.1093/nar/22.22.4673.
54. Hall T. Bioedit: A user friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Serials 1999, 41:95-98.
55. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120. 10.1007/BF01731581, 7463489.
56. Kumar S, Tamura K, Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 2004, 5:150-163. 10.1093/bib/5.2.150, 15260895.
57. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214. 2247476, 17996036, 10.1186/1471-2148-7-214.
58. Sonnhammer EL, Durbin R. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 1995, 167:GC1-10. 10.1016/0378-1119(95)00714-8, 8566757.