Evolution of HLA-DRB genes

Molecular Biology and Evolution

Volumn 29, Issue 12, 2012, Pages 3843-3853

  Doxiadis, Gaby G M ^a   Hoof, Ilka ^b   De Groot, Nanine ^a   Bontrop, Ronald E ^a,b  

^a BIOMEDICAL PRIMATE RESEARCH CENTRE   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

evolution; HLA; introns; MHC; primates; transposable elements

Indexed keywords

HLA DR ANTIGEN; HLA DRB ANTIGEN; HLA DRB1 ANTIGEN; HLA DRB3 ANTIGEN; HLA DRB4 ANTIGEN; HLA DRB5 ANTIGEN; UNCLASSIFIED DRUG;

CERCOPITHECIDAE; CONFERENCE PAPER; GENE INSERTION; GENE LOCUS; GENE MUTATION; GENE POOL; HOMINID; HUMAN; INTRON; LONG INTERSPERSED REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLATYRRHINI; PSEUDOGENE; SHORT INTERSPERSED REPEAT; TRANSPOSON;

ANIMALS; BASE SEQUENCE; CALLITHRIX; CLUSTER ANALYSIS; DNA PRIMERS; EVOLUTION, MOLECULAR; HLA-DR BETA-CHAINS; HUMANS; INTRONS; LIKELIHOOD FUNCTIONS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MACACA MULATTA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PAN TROGLODYTES; PHYLOGENY; PSEUDOGENES; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

CALLITHRIX JACCHUS; CERCOPITHECIDAE; HOMINIDAE; MACACA MULATTA; PAN; PRIMATES;

EID: 84869022981     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss186     Document Type: Conference Paper

References (59)

1. Andersson G, Larhammar D,Widmark E, Servenius B, Peterson PA, Rask L. 1987. Class II genes of the human major histocompatibility complex. Organization and evolutionary relationship of the DR beta genes. J Biol Chem. 262:8748-8758.
2. Andersson G, Svensson AC, Setterblad N, Rask L. 1998. Retroelements in the human MHC class II region. Trends Genet. 14:109-114.
3. Antunes SG, de Groot NG, Brok H, Doxiadis G, Menezes AA, Otting N, Bontrop RE. 1998. The common marmoset: a new world primate species with limited Mhc class II variability. Proc Natl Acad Sci U S A. 95:11745-11750.
4. Bannert N, Kurth R. 2004. Retroelements and the human genome: new perspectives on an old relation. Proc Natl Acad Sci U S A. 101(2 Suppl), 14572-14579.
5. Bannert N, Kurth R. 2006. The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet. 7:149-173.
6. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet. 3:370-379.
7. Belancio VP, Hedges DJ, Deininger P. 2008. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res. 18:343-358.
8. Bergstrom TF, Josefsson A, Erlich HA, Gyllensten U. 1998. Recent origin of HLA-DRB1 alleles and implications for human evolution. Nat Genet. 18:237-242.
9. Blancher A, Tisseyre P, Dutaur M, Apoil PA, Maurer C, Quesniaux V, Raulf F, Bigaud M, Abbal M. 2006. Study of Cynomolgus monkey (Macaca fascicularis) MhcDRB (Mafa-DRB) polymorphism in two populations. Immunogenetics 58:269-282.
10. Bontrop RE, Otting N, de Groot NG, Doxiadis GG. 1999. Major histocompatibility complex class II polymorphisms in primates. Immunol Rev. 167:339-350.
11. Brandle U, Ono H, Vincek V, Klein D, Golubic M, Grahovac B, Klein J. 1992. Trans-species evolution of Mhc-DRB haplotype polymorphism in primates: organization of DRB genes in the chimpanzee. Immunogenetics 36:39-48.
12. Britten RJ. 2010. Transposable element insertions have strongly affected human evolution. Proc Natl Acad Sci U S A. 107:19945-19948.
13. de Groot N, Doxiadis GG, de Vos-Rouweler AJ, de Groot NG, Verschoor EJ, Bontrop RE. 2008. Comparative genetics of a highly divergent DRB microsatellite in different macaque species. Immunogenetics 60: 737-748.
14. de Groot NG, Heijmans CM, de Groot N, Doxiadis GG, Otting N, Bontrop RE. 2009. The chimpanzee Mhc-DRB region revisited: gene content, polymorphism, pseudogenes, and transcripts. Mol Immunol. 47:381-389.
15. de Groot NG, Otting N, Robinson J, et al (11 co-authors). 2012. Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and NewWorld monkey species. Immunogenetics 64:615-631.
16. Deininger PL, Batzer MA. 2002. Mammalian retroelements. Genome Res. 12:1455-1465.
17. Doxiadis GG, de Groot N, Bontrop RE. 2008. Impact of endogenous intronic retroviruses on major histocompatibility complex class II diversity and stability. J Virol. 82:6667-6677.
18. Doxiadis GG, de Groot N, de Groot NG, Doxiadis II, Bontrop RE. 2008. Reshuffling of ancient peptide binding motifs between HLA-DRB multigene family members: old wine served in new skins. Mol Immunol. 45:2743-2751.
19. Doxiadis GG, Rouweler AJ, de Groot NG, Louwerse A, Otting N, Verschoor EJ, Bontrop RE. 2006. Extensive sharing of MHC class II alleles between rhesus and cynomolgus macaques. Immunogenetics 58:259-268.
20. Erlich HA, Bergstrom TF, StonekingM, Gyllensten U. 1996. HLA sequence polymorphism and the origin of humans. Science 274:1552b-155
21. b. Fernandez-Soria VM, Morales P, Castro MJ, Suarez B, Recio MJ, Moreno MA, Paz-Artal E, Arnaiz-Villena A. 1998. Transcription and weak expression of HLA-DRB6: a gene with anomalies in exon 1 and other regions. Immunogenetics 48:16-21.
22. Figueroa F, O'HUigin C, Tichy H, Klein J. 1994. The origin of the primate Mhc-DRB genes and allelic lineages as deduced from the study of prosimians. J Immunol. 152:4455-4465.
23. Glazko GV, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol Biol Evol. 20:424-434.
24. Gongora R, Figueroa F, Klein J. 1997. Complex origin of the HLA-DR10 haplotype. J Immunol. 159:6044-6051.
25. Gongora R, Figueroa F, O'Huigin C, Klein J. 1997. HLA-DRB9-possible remnant of an ancient functional DRB subregion. Scand J Immunol. 45:504-510.
26. Goodier JL, Kazazian HH Jr. 2008. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135:23-35.
27. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
28. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
29. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. 2007. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 8:460.
30. Iskow RC, McCabe MT,Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. 2010. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141: 1253-1261.
31. Jurka J, Smith T. 1988. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A. 85:4775-4778.
32. Kazazian HH Jr. 2004. Mobile elements: drivers of genome evolution. Science 303:1626-1632.
33. Kenter M, Otting N, Anholts J, Jonker M, Schipper R, Bontrop RE. 1992. Mhc-DRB diversity of the chimpanzee (Pan troglodytes). Immunogenetics 37:1-11.
34. Klein D, Vincek V, Kasahara M, Schonbach C, O'HUigin C, Klein J. 1991. Gorilla major histocompatibility complex-DRB pseudogene orthologous to HLA-DRBVIII. Hum Immunol. 32:211-220.
35. Klein J, O'HUigin C. 1995. Class II B Mhc motifs in an evolutionary perspective. Immunol Rev. 143:89-111.
36. Klein J, Sato A, Nikolaidis N. 2007. MHC, TSP, and the origin of species: from immunogenetics to evolutionary genetics. Annu Rev Genet. 41: 281-304.
37. Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7:474.
38. Kriener K, O'HUigin C, Klein J. 2000. Alu elements support independent origin of prosimian, platyrrhine, and catarrhine Mhc-DRB genes. Genome Res. 10:634-643.
39. Kriener K, O'HUigin C, Tichy H, Klein J. 2000. Convergent evolution of major histocompatibility complex molecules in humans and New World monkeys. Immunogenetics 51:169-178.
40. Levin HL, Moran JV. 2011. Dynamic interactions between transposable elements and their hosts. Nat Rev Genet. 12:615-627.
41. Marsh SG, Albert ED, Bodmer WF, et al (24 co-authors). 2010. Nomenclature for factors of the HLA system, 2010. Tissue Antigens 75:291-455.
42. Mayer WE, O'HUigin C, Klein J. 1993. Resolution of the HLA-DRB6 puzzle: a case of grafting a de novo-generated exon on an existing gene. Proc Natl Acad Sci U S A. 90:10720-10724.
43. Mayer WE, O'HUigin C, Zaleska-Rutczynska Z, Klein J. 1992. Trans-species origin of Mhc-DRB polymorphism in the chimpanzee. Immunogenetics 37:12-23.
44. McClintock B. 1956. Intranuclear systems controlling gene action and mutation. Brookhaven Symp Biol. pp. 58-74.
45. Mnukova-FajdelovaM, Satta Y, O'HUigin C, MayerWE, Figueroa F, Klein J. 1994. Alu elements of the primate major histocompatibility complex. Mamm Genome. 5:405-415.
46. Munoz-Lopez M, Macia A, Garcia-Canadas M, Badge RM, Garcia-Perez JL. 2011. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans. Mob Genet Elements. 1: 122-127.
47. O'Connor SL, Blasky AJ, Pendley CJ, Becker EA, Wiseman RW, Karl JA, Hughes AL, O'Connor DH. 2007. Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques. Immunogenetics 59:449-462.
48. Oliver KR, Greene WK. 2011. Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA 2:8.
49. Perelman P, Johnson WE, Roos C, et al. (11 co-authors). 2011. A molecular phylogeny of living primates. PLoS Genet. 7: e1001342.
50. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253-1256.
51. Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SG. 2003. IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res. 31:311-314.
52. Rodriguez F, Oliver JL, Marin A, Medina JR. 1990. The general stochastic model of nucleotide substitution. J Theor Biol. 142:485-501.
53. Satta Y, Mayer WE, Klein J. 1996. Evolutionary relationship of HLA-DRB genes inferred from intron sequences. J Mol Evol. 42:648-657.
54. Sawai H, Kawamoto Y, Takahata N, Satta Y. 2004. Evolutionary relationships of major histocompatibility complex class I genes in simian primates. Genetics 166:1897-1907.
55. Schonbach C, Vincek V,Mayer WE, Golubic M, O'HUigin C, Klein J. 1993. Multiplication of Mhc-DRB5 loci in the orangutan: implications for the evolution of DRB haplotypes. Mamm Genome. 4:159-170.
56. Slierendregt BL, Otting N, van Besouw N, Jonker M, Bontrop RE. 1994. Expansion and contraction of rhesus macaque DRB regions by duplication and deletion. J Immunol. 152:2298-2307.
57. Smit AF. 1996. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 6:743-748.
58. van Rood JJ, van Leeuwen A, Keuning JJ, Termijtelen A. 1977. Evidence for two series of B-cell antigens in man and their comparison with HLA-D. Scand J Immunol. 6:373-384.
59. Xing J, Zhang Y, Han K, et al (11 co-authors). 2009. Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 19:1516-1526.