Nucleotide sequencing analysis of the 146-kilobase segment around the IkBL and MICA genes at the centromeric end of the HLA class I region

Genomics

Volumn 47, Issue 3, 1998, Pages 372-382

  Shiina, Takashi ^a   Tamiya, Gen ^a   Oka, Akira ^a   Yamagata, Tetsushi ^c   Yamagata, Naomi ^a   Kikkawa, Eri ^a   Goto, Kaori ^a   Mizuki, Nobuhisa ^a   Watanabe, Koji ^b   Fukuzumi, Yasuhito ^b   Taguchi, Susumu ^b   Sugawara, Chiyo ^b   Ono, Ayako ^b   Chen, Lei ^a   Yamazaki, Masaaki ^b   Tashiro, Hiroyuki ^b   Ando, Asako ^a   Ikemura, Toshimichi ^c   Kimura, Minoru ^a   Inoko, Hidetoshi ^a  

^a TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^b Fujiya Co Ltd   (Japan)

^c NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; HLA ANTIGEN CLASS 1;

ANIMAL CELL; ARTICLE; CENTROMERE; CHROMOSOME 6; DNA SEQUENCE; GENE DUPLICATION; GENE ISOLATION; GENE MAPPING; HLA SYSTEM; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; YEAST ARTIFICIAL CHROMOSOME;

EID: 0032006134     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1997.5114     Document Type: Article

References (63)

1. Abderrahim H., Sambucy J. L., Iris F., Ougen P., Billault A., Chumakov I. M., Dausset J., Cohen D., Le-Paslier D. Cloning the human major histocompatibility complex in YACs. Genomics. 23:1994;520-527.
2. Albertalla M. R., Campbell R. D. Characterization of a novel gene in the human major histocompatibility complex that encodes a potential new member of the I kappa B family of proteins. Hum. Mol. Genet. 3:1994;793-799.
3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
4. Ando H., Mizuki N., Ota M., Yamazaki M., Ohno S., Goto K., Miyata Y., Wakisaka K., Mahram S., Inoko H. Allelic variations of humanMHC. Immunogenetics. 1997.
5. Avoustin P., Ribouchon M. T., Vernet C., N'Guyen B., Crouau-Roy B., Pontarotti P. Non-homologous recombination within the major histocompatibility complex creates a transcribed hybrid sequence. Mamm. Genome. 5:1994;771-776.
6. Bahram S., Bresnahan M., Geraghty D. E., Spies T. A second lineage of mammalian major histocompatibility complex class I genes. Proc. Natl. Acad. Sci. USA. 91:1994;6259-6263.
7. Bahram S., Mizuki N., Inoko H., Spies T. Nucleotide sequence of the humanMHCMICA. Immunogenetics. 44:1996a;80-81.
8. Bahram S., Shiina T., Tamiya G., Oka A., Inoko H. Genomic structure of the humanMHCMICB. Immunogenetics. 45:1996b;161-162.
9. Bernardi G. The human genome: Organization and evolutionary history. Annu. Rev. Genet. 29:1995;443-476.
10. Bird A. P. CpG-rich islands and the function of DNA methylation. Nature. 321:1986;209-213.
11. Bouissou C., Pontarotti P., Crouau-Roy B. A precise meiotic map in the class I region of the human major histocompatibility complex. Genomics. 30:1995;486-492.
12. Burt M. J., Smit D. J., Pyper W. R., Powell L. W., Jazwinska E. C. A 4.5-megabase YAC contig and physical map over the haemochromatosis gene region. Genomics. 33:1996;153-158.
13. Campbell R. D., Trowsdale J. A map of the human major histocompatibility complex. Immunol. Today. 18:1997.
14. Chu T. W., Capossela A., Coleman R., Goei V. L., Nallur G., Gruen J. R. Cloning of a new finger protein gene (ZNF173MHC. Genomics. 29:1995;229-239.
15. Cross S. H., Charlton J. A., Nan X., Bird A. P. Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 6:1994;236-244.
16. Crouau-Roy B., Amadou C., Bouissou C., Clayton J., Vernet C., Ribouchon M. T., Pontarotti P. Localization of theOTF3MHC. Genomics. 21:1994;241-243.
17. Deininger P. L. Random subcloning of sonicated DNA: Application to shotgun DNA sequence analysis. Anal. Biochem. 129:1983;216-223.
18. Fan W., Cai W., Parimoo S., Lennon G. G., Weissman S. M. Identification of seven new humanMHCHLA-F. Immunogenetics. 44:1996;97-103.
19. Feder J. N., Gnirke A., Thomas W., Tsuchihashi Z., Ruddy D. A., Basava A., Dormishian F., Domingo R. Jr., Ellis M. C., Fullan A., Hinton L. M., Jones N. L., Kimmel B. E., Kronmal G. S., Lauer P., Lee V. K., Loeb D. B., Mapa F. A., McClelland E., Meyer N. C., Mintier G. A., Moeller N., Moore T., Morikang E., Prass C. E., Quintana L., Starnes S. M., Schatzman R. C., Brunke K. J., Drayna D. T., Risch N. J., Bacon B. R., Wolff R. K. A novelMHC. Nat. Genet. 13:1996;399-408.
20. Fischer G., Wittmann-Liebold B., Lang K., Kiefhaber T., Schmid F. X. Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature. 337:1989;476-478.
21. Fukagawa T., Sugaya K., Matsumoto K., Okumura K., Ando A., Inoko H., Ikemura T. A boundary of long-range G+C% mosaic domains in the humanMHC. Genomics. 25:1995;184-191.
22. Gardiner-Garden M., Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 196:1987;261-282.
23. Geraghty D. E. Structure of theHLA. Curr. Biol. 5:1992;3-7.
24. Geraghty D. E., Koller B. H., Pei J., Hansen J. A. Examination of fourHLAHLA. J. Immunol. 149:1992a;1947-1956.
25. Geraghty D. E., Pei J., Lipsky B., Hansen J. A., Taillon-Miller P., Bronson S. K., Chaplin D. D. Cloning and physical mapping of theHLAHLA-EHLA-F. Proc. Natl. Acad. Sci. USA. 89:1992b;2669-2673.
26. Giffon T., Lepourcelet M., Pichon L., Jezequel P., Bouric P., Carn G., Pontarotti P., Le Gall J. Y., David V. Cloning of a human homologue of the mouseTctex-5MHC. Immunogenetics. 44:1996;331-339.
27. Gillies S. D., Folsom V., Tonegawa S. Cell type-specific enhancer element associated with a mouseMHCE. Nature. 310:1984;594-597.
28. Goei V. L., Parimoo S., Capossela A., Chu T. W., Gruen J. R. Isolation of novel non-HLA gene fragments from the haemochromatosis region (6p21.3) by cDNA hybridization selection. Am. J. Hum. Genet. 54:1994;244-251.
29. Gruen J. R., Goei V. L., Summers K. M., Capossela A., Powell L., Halliday J., Zoghbi H., Shukla H., Weissman S. M. Physical and genetic mapping of the telomeric major histocompatibility complex region in man and relevance to the primary haemochromatosis gene (HFE). Genomics. 14:1992;232-240.
30. Gruen J. R., Nalabolu S. R., Chu T. W., Bowlus C., Fan W. F., Goei V. L., Wei H., Sivakamasundari R., Liu Y. C., Xu H. X., Parimoo S., Nallur G., Ajioka R., Shukla H., Bray-ward P., Pan J., Weissman S. M. A transcription map of the major histocompatibility complex (MHC. Genomics. 36:1996;70-85.
31. Iris J. M., Bougueleret L., Prieur S., Caterina D., Primas G., Perrot V., Jurka J., Rodriguez-Tome P., Claverie J. M., Dausset J., Cohen D. DenseAlu. Nat. Genet. 3:1993;137-145.
32. Kasahara M., Hayashi M., Tanaka K., Inoko H., Sugaya K., Ikemura T., Ishibashi T. Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex. Proc. Natl. Acad. Sci. USA. 93:1996;9096-9101.
33. Koop B. F., Rowan L., Chen W. Q., Deshpande P., Lee H., Hood L. Sequence length and error analysis of sequenase and automatedTaq. Biotechniques. 14:1993;442-447.
34. Krishnan B. R., Jamry I., Chaplin D. D. Feature mapping of theHLAPOU5F1TCF19. Genomics. 30:1995a;53-58.
35. Krishnan B. R., Jamry I., Berg D. E., Berg C. M., Chaplin D. D. Construction of a genomic DNA feature map by sequencing from nested deletions: Application to theHLA. Nucleic Acids Res. 23:1995b;117-122.
36. Leelayuwat C., Pinelli M., Dawkins R. L. Clustering of diverse replicated sequences in theMHC. J. Immunol. 155:1995;692-698.
37. Lepourcelet M., Andrieux N., Giffon T., Pichon L., Hampe A., Galibert F., Mosser J. Systematic sequencing of the humanHLA-A/HLA-F. Genomics. 37:1996;316-326.
38. Mizuki N., Ota M., Kimura M., Ohno S., Ando H., Katsuyama Y., Yamazaki M., Watanabe K., Goto K., Nakamura S., Bahram S., Inoko H. Triplet repeat polymorphism in the transmembrane region of theMICA. Proc. Natl. Acad. Sci. USA. 94:1997a;1298-1303.
39. Mizuki N., Ando H., Kimura M., Ohno S., Miyata S., Yamazaki M., Tashiro H., Watanabe K., Ono A., Taguchi S., Sugawara C., Fukuzumi Y., Okumura K., Goto K., Ishihara M., Kikuti Y., Shiina T., Lei C., Ando A., Ikemura T., I-noko H. Nucleotide sequence analysis of theHLAHLA-B-C. Genomics. 42:1997b;55-66.
40. Nalabolu S. R., Shukla H., Nallur G., Parimoo S., Weissman S. M. Genes in a 220 kb region spanning the TNF cluster in human MHC. Genomics. 31:1996;215-222.
41. Ota M., Katsuyama Y., Mizuki N., Ando H., Furihata K., Ono S., Pivetti-Pezzi P., Tabbara K. F., Palimeris G. D., Nikbin B., Davatchi F., Chams H., Geng Z., Bahram S., Inoko H. Trinucleotide repeat polymorphism within exon 5 of theMICAMHC. Tissue Antigens. 49:1997;448-454.
42. Peelman L. J., Chardon P., Nunes M., Renard C., Geffrotin C., Vaiman M., Zeveren A. V., Coppieters W., Weghe A. V., Bouquet Y., Choy W. W., Strominger J. L., Spies T. TheBAT1MHC. Genomics. 26:1995;210-218.
43. Pham-Dinh D., Mattei M. G., Nussbaum J. L., Roussel G., Pontarotti P., Roeckel N., Mather I. H., Artzt K., Lindahl K. F., Dautigny A. Myelin/oligodendrocyte glycoprotein is a member of a subset of the immunoglobulin superfamily encoded within the major histocompatibility complex. Proc. Natl. Acad. Sci. USA. 90:1993;7990-7994.
44. Pham-Dinh D., Jones E. P., Pitiot G., Gaspera B. D., Daubas P., Mallet J., Paslier D. L., Lindahl K. F., Dautigny A. Physical mapping of the human and mouseMOGMHC. Immunogenetics. 42:1995;386-391.
45. Pichon L., Hampe A., Giffon T., Carn G., Legall J. Y., David V. A new non-HLA multigene family associated with thePERB11MHC. Immunogenetics. 44:1996;259-267.
46. Rowen L., Koop B., Hood L. The complete 685-kilobase DNA sequence of the human βT cell receptor locus. Science. 272:1996;1755-1762.
47. Satyanarayama K., Strominger J. L. DNA sequences near a meiotic recombinational breakpoint within the humanHLA-DQ. Immunogenetics. 35:1992;235-240.
48. Smith T. M., Lee M. K., Szabo C. I., Jerome N., McEuen M., Taylor M., Hood L., King M. C. Complete genomic sequence and analysis of 117 kb of human DNA containing the geneBRCA1. Genome Res. 6:1996;1029-1049.
49. Solovyev V. V., Salamov A. A., Lawrence C. B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22:1994;5156-5163.
50. Takahashi N., Hayano T., Suzuki M. Peptidyl-prolyl cis-trans isomerase is the cyclospolin A-binding protein cyclophilin. Nature. 337:1989;473-475.
51. Tirosvoutis K. N., Divane A., Jones M., Affara N. A. Characterization of a novel zinc finger gene (ZNF165) mapping to 6p21 that is expressed specifically in testis. Genomics. 28:1995;485-490.
52. Totaro A., Grifa A., Roetto A., Lunardi C., D'Agruma L., Sbaiz L., Zelante L., Sandre G. D., Camaschella C., Gasparini P. New polymorphisms and markers in theHLA. Hum. Genet. 95:1995;429-434.
53. Totaro A., Rommens J. M., Grifa A., Lunardi C., Carella M., Huizenga J. J., Roetto A., Camaschella C., Sandre G. D., Gasparini P. Hereditary haemochromatosis: Generation of a transcription map within a refined and extended map of theHLA. Genomics. 31:1996;319-326.
54. Treco D., Arnheim N. The evolutionarily conserved repetitive sequence d(TG.AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis. Mol. Cell Biol. 6:1986;3934-3947.
55. Uberbacher E. C., Mural R. J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA. 88:1991;11261-11265.
56. Venditti C. P., Harris J. M., Geraghty D. E., Chorney M. J. Mapping and characterization of non-HLAMHC. Genomics. 22:1994;257-266.
57. Vernet C., Ribouchon M. T., Chimini G., Jouanolle A. M., Sidibe I., Pontarotti P. A novel coding sequence belonging to a new multicopy gene family mapping within the humanMHC. Immunogenetics. 38:1993;47-53.
58. Vernet C., Ribouchon M. T., Chimini G., Pontarotti P. Structure and evolution of a member of a new subfamily of GTP-binding proteins mapping to the humanMHC. Mamm. Genome. 5:1994;100-105.
59. Volz A., Weiss E., Trowsdale J., Zieglar A. Presence of an expressed β-tubulin gene (TUBBHLA. Hum. Genet. 93:1994;42-46.
60. Wei H., Fan W. F., Xu H., Parimoo S., Shukla H., Chaplin D. D., Weissman S. M. Genes in one megabase of theHLA. Proc. Natl. Acad. Sci. USA. 90:1993;11870-11874.
61. Wilson R. K., Koop B. F., Chen C., Halloran N., Sciammis R., Hood L. Nucleotide sequence analysis of 95 kb near the 3′ end of the murine T-cell receptor α/δ chain locus: Strategy and methodology. Genomics. 13:1992;1198-1208.
62. Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J., Burton J., Connell M., Copsey T., Cooper J. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature. 368:1994;32-38.
63. Zhou Y., Chaplin D. D. Identification in theHLA. Proc. Natl. Acad. Sci. USA. 90:1993;9470-9474.