HLA-H: A pseudogene with increased variation due to balancing selection at neighboring loci

Molecular Biology and Evolution

Volumn 15, Issue 12, 1998, Pages 1581-1588

  Grimsley, Carrie ^a,b   Mather, Kristie A ^a,c   Ober, Carole ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Apes; Balancing selection; HLA H; Humans; Pseudogene

Indexed keywords

DNA;

ARTICLE; DNA SEQUENCE; GENE LOCUS; GENE MUTATION; GENOME; HLA SYSTEM; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIMATE; PSEUDOGENE; SPECIES DIFFERENCE;

PRIMATES;

EID: 0031773259     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025886     Document Type: Article

References (37)

1. ALIZADEH, M., C. LEGRAS, G. SEMANA, P. LE BOUTEILLER, B. GENETET, and R. FAUCHET. 1993. Evidence for a polymorphism of HLA-G gene. Hum. Immunol. 38:206-212.
2. ARNETT, K. L., and P. PARHAM. 1995. HLA class I nucleotide sequences, 1995. Tissue Antigens 45:217-257.
3. BJORKMAN, P. J., M. A. SAPER, B. SAMRAOUI, W. S. BENNETT, J. L. STROMINGER, and D. C. WILEY. 1987. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329:506-512.
4. CARROLL, M. C., P. KATZMAN, E. M. ALICOT, B. H. KOLLER, D. E. GERAGHTY, H. T. ORR, J. L. STROMINGER, and T. SPIES. 1987. Linkage map of the human major histocompatibility complex including the tumor necrosis factor genes. Proc. Natl. Acad. Sci. USA 84:8535-8539.
5. CHAKRAVARTI, A., J. A. PHILLIPS III, K. H. MELLITS, K. H. BUETOW, and P. H. SEEBURG. 1984. Patterns of polymorphism and linkage disequilibrium suggest independent origins of the human growth hormone gene cluster. Proc. Natl. Acad. Sci. USA 81:6085-6089.
6. CHORNEY, M. J., I. SAWADA, G. A. GILLESPIE, R. SRIVASTAVA, J. PAN, and S. M. WEISSMAN. 1990. Transcription analysis, physical mapping, and molecular characterization of a non-classical human leukocyte antigen class I gene. Mol. Cell. Biol. 10:243-253.
7. CLARK, A., and T. KAO. 1991. Excess nonsynonymous substitutions at shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proc. Natl. Acad. Sci. USA 88: 9823-9827.
8. DOHERTY, P. C., and R. M. ZINKERNAGEL. 1975. A biological role for the major histocompatibility antigens. Lancet I: 1406-1409.
9. GRIMSLEY, C. 1997. The nature of selection acting on the class Ib HLA genes: HLA-E, HLA-F, and HLA-G. Ph.D. thesis, University of Chicago, Chicago.
10. GRIMSLEY, C., and C. OBER. 1997. Population genetic studies of HLA-E: evidence for selection. Hum. Immunol. 52:33-40.
11. HUDSON, R. R., and N. L. KAPLAN. 1988. The coalescent process in models with selection and recombination. Genetics 120:831-840.
12. HUDSON, R. R., M. KREITMAN, and M. AGUADE. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153.
13. HUGHES, A. L., and M. NEI. 1989. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86: 958-962.
14. HUGHES, A. L., T. OHTA, and M. NEI. 1990. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major histocompatibility complex molecules. Mol. Biol. Evol. 7:515-524.
15. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
16. KIMURA, M., and T. OHTA. 1972. On the stochastic model for estimation of mutational distance between homologous proteins. J. Mol. Evol. 2:87-90.
17. KOEBERL, D. D., C. D. K. BOTTEMA, J. BUERSTEDDE, and S. S. SOMMER. 1989. Functionally important regions of the factor IX gene have a low rate of polymorphism and a high rate of mutation in the dinucleotide CpG. Am. J. Hum. Genet. 45:448-457.
18. KREITMAN, M. 1983. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304:412-417.
19. KREITMAN, M., and R. R. HUDSON. 1991. Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics 127:565-582.
20. LAWLOR, D. A., E. WARREN, P. TAYLOR, and P. PARHAM. 1991. Gorilla class I major histocompatibility complex alleles: comparison to human and chimpanzee class I. J. Exp. Med. 174:1491-1509.
21. Li, W. H., and L. A. SADLER. 1991. Low nucleotide diversity in man. Genetics 129:513-523.
22. MCDONALD, J. H., and M. KREITMAN. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
23. NEI, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
24. NEI, M., and A. L. HUGHES. 1991. Polymorphism and evolution of the major histocompatibility complex loci in mammals. Pp. 222-247 in R. K. SELANDER, A. G. CLARK, and T. S. WHITTAM, eds. Evolution at the molecular level. Sinauer, Sunderland, Mass.
25. OBER, C., B. ROSINSKY, C. GRIMSLEY, A. ROBERTSON, and A. RUNGE. 1996. Population genetic studies of HLA-G: allele frequencies and linkage disequilibrium with HLA-A. J. Reprod. Immunol. 32:111-123.
26. PARHAM, P. 1995. Antigen presentation by class I major histocompatibility complex molecules: a context for thinking about HLA-G. Am. J. Reprod. Immunol. 34:10-19.
27. PARHAM, P., and T. OHTA. 1996. Population biology of antigen presentation by MHC class I molecules. Science 272:67-74.
28. RICHMAN, R., M. UYENOYAMA, and J. KOHN. 1996. Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. Science 273:1212-1216.
29. ROZAS, J., and R. ROZAS. 1997. DnaSP version 2.0: a novel software package for extensive molecular population genetic analysis. Comput. Appl. Biosci. 13:307-311.
30. SHUKLA, H., G. A. GILLESPIE, R. SRIVASTAVA, F. COLLINS, and M. J. CHORNEY. 1991. A class I jumping clone places the HLA-G gene approximately 100 kilobases from HLA-H within the HLA-A subregion of the human MHC. Genomics 10:905-914.
31. SIMONSEN, K. L., G. A. CHURCHILL, and C. F. AQUADRO. 1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141:413-429.
32. STROBECK, C. 1983. Expected linkage disequilibrium for a neutral locus linked to a chromosomal arrangement. Genetics 103:545-555.
33. TAJIMA, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
34. VAN DER VEN, K., and C. OBER. 1994. HLA-G polymorphisms in African Americans. J. Immunol. 153:5628-5633.
35. VENDITTI, C. P., and M. J. CHORNEY. 1992. Class I gene contraction within the HLA-A subregion of the human MHC. Genomics 14:1003-1009.
36. YAMASHITA, T., T. FUJII, Y. WATANABE, K. TOKUNAGA, K. TADOKORO, T. JUJI, and Y. TAKETANI. 1996. HLA-G gene polymorphism in a Japanese population. Immunogenetics 44:186-191.
37. ZEMMOUR, J., B. H. KOLLER, P. D. ENNIS, D. E. GERAGHTY, D. A. LAWLOR, H. T. ORR, and P. PARHAM. 1990. HLA-AR, an inactivated antigen-presenting locus related to HLA-A. J. Immunol. 144:3619-3629.