Sequence analysis of an 800-kb genomic DNA region on chromosome 8q21 that contains the Nijmegen breakage syndrome gene, NBS1

被引:19
作者
Tauchi, H
Matsuura, S
Isomura, M
Kinjo, T
Nakamura, A
Sakamoto, S
Kondo, N
Endo, S
Komatsu, K
Nakamura, Y
机构
[1] Univ Tokyo, Inst Med Sci, Mol Med Lab, Minato Ku, Tokyo 1088639, Japan
[2] Hiroshima Univ, Res Inst Radiat Biol & Med, Minami Ku, Hiroshima 7348553, Japan
基金
日本科学技术振兴机构;
关键词
D O I
10.1006/geno.1998.5657
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
An 800-kb region on chromosome 8q21, which complements the phenotype of cells from Nijmegen breakage syndrome patients, is a candidate for the locus of the underlying gene, termed NBS1. The sequence of this 800-kb region of DNA indicated that the size of this segment is 755,832 bp with an additional 36-kb gap. From this region, we identified four genes including NBS1, a gene coding for a 27-kDa vitamin D-dependent calcium-binding protein (27-kDa calbindin), the mitochondrial 2,4-dienoyl-CoA reductase gene, and a novel gene, C8orf1/hT41. All four genes were aligned in a 250-kb centromeric portion of the region, and no gene was found in the remaining telomeric portion containing 500 kb. The genomic organization of the C8orf1/hT41 and NBS1 genes has been analyzed using the computer programs GRAIL 2 and GENSCAN. They predicted and successfully found more than 93% of the exons, even a small 54-bp exon, indicating that one or more exons in any gene can be identified by these programs. GENSCAN was more efficient at locating the four genes than GRAIL 2 and identified 15 of the 16 exons of the NBS1 gene. This 800-kb region contained repetitive sequences, including 179 copies of the Alu sequence (1 copy/4.2 kb), 123 copies of the L1 sequence (1 copy/6.1 kb), 107 copies of the LTR sequence (1 copy/7.1 kb), and 63 copies of the MER sequence (1 copy/12 kb). There was a slight but not significant difference in the repetitive content of the gene-rich region and the remaining noncoding region. Our results indicate that computer-assisted methods are useful and powerful for identifying exons of both known and novel genes. (C) 1999 Academic Press.
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页码:242 / 247
页数:6
相关论文
共 16 条
  • [1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Altschul, SF
    Madden, TL
    Schaffer, AA
    Zhang, JH
    Zhang, Z
    Miller, W
    Lipman, DJ
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (17) : 3389 - 3402
  • [2] Prediction of complete gene structures in human genomic DNA
    Burge, C
    Karlin, S
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1997, 268 (01) : 78 - 94
  • [3] Fine localization of the Nijmegen breakage syndrome gene to 8q21:: Evidence for a common founder haplotype
    Cerosaletti, KM
    Lange, E
    Stringham, HM
    Weemaes, CMR
    Smeets, D
    Sölder, B
    Belohradsky, BH
    Taylor, AMR
    Karnes, P
    Elliott, A
    Komatsu, K
    Gatti, RA
    Boehnke, M
    Concannon, P
    [J]. AMERICAN JOURNAL OF HUMAN GENETICS, 1998, 63 (01) : 125 - 134
  • [4] Molecular cloning and characterization of the human mitochondrial 2,4-dienoyl-CoA reductase gene (DECR)
    Helander, HM
    Koivuranta, KT
    HorelliKuitunen, N
    Palvimo, JJ
    Palotie, A
    Hiltunen, JK
    [J]. GENOMICS, 1997, 46 (01) : 112 - 119
  • [5] Identification and characterization of a new gene physically linked to the ATM gene
    Imai, T
    Yamauchi, M
    Seki, N
    Sugawara, T
    Saito, T
    Matsuda, Y
    Ito, H
    Nagase, T
    Nomura, N
    Hori, TA
    [J]. GENOME RESEARCH, 1996, 6 (05) : 439 - 447
  • [6] Positional cloning of the gene for Nijmegen breakage syndrome
    Matsuura, S
    Tauchi, H
    Nakamura, A
    Kondo, N
    Sakamoto, S
    Endo, S
    Smeets, D
    Solder, B
    Belohradsky, BH
    Kaloustian, VMD
    Oshimura, M
    Isomura, M
    Nakamura, Y
    Komatsu, K
    [J]. NATURE GENETICS, 1998, 19 (02) : 179 - 181
  • [7] Genetic mapping using microcell-mediated chromosome transfer suggests a locus for Nijmegen breakage syndrome at chromosome 8q21-24
    Matsuura, S
    Weemaes, C
    Smeets, D
    Takami, H
    Kondo, N
    Sakamoto, S
    Yano, N
    Nakamura, A
    Tauchi, H
    Endo, S
    Oshimura, M
    Komatsu, K
    [J]. AMERICAN JOURNAL OF HUMAN GENETICS, 1997, 60 (06) : 1487 - 1494
  • [8] A KNOWLEDGE BASE FOR PREDICTING PROTEIN LOCALIZATION SITES IN EUKARYOTIC CELLS
    NAKAI, K
    KANEHISA, M
    [J]. GENOMICS, 1992, 14 (04) : 897 - 911
  • [9] THE HUMAN CALBINDIN 27-KDA GENE - STRUCTURAL ORGANIZATION OF THE 5' AND 3' REGIONS, CHROMOSOMAL ASSIGNMENT, AND RESTRICTION FRAGMENT LENGTH POLYMORPHISM
    PARMENTIER, M
    DEVIJLDER, JJM
    MUIR, E
    SZPIRER, C
    ISLAM, MQ
    VANKESSEL, AG
    LAWSON, DEM
    VASSART, G
    [J]. GENOMICS, 1989, 4 (03) : 309 - 319
  • [10] Identification of the murine beige gene by YAC complementation and positional cloning
    Perou, CM
    Moore, KJ
    Nagle, DL
    Misumi, DJ
    Woolf, EA
    McGrail, SH
    Holmgren, L
    Brody, TH
    Dussault, BJ
    Monroe, CA
    Duyk, GM
    Pryor, RJ
    Li, LT
    Justice, MJ
    Kaplan, J
    [J]. NATURE GENETICS, 1996, 13 (03) : 303 - 308