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Identification of a human specificAlu insertion in the factor XIIIB gene

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Abstract

The factor XIIIB gene was examined to determine the nature of a previously described 300 bp restriction fragment length polymorphism (RFLP) seen in the human population. Polymerase chain reaction analysis of different regions within the factor XIIIB gene was carried out to define a high resolution map of the region encompassing the polymorphism, followed by DNA sequence analysis. AnAlu insertion was found to be the source of this variation. ThisAlu repeat is a member of the human specific-1 (HS-1) subfamily, although one of the five diagnostic nucleotides is a cattarhine specific (CS) subfamily mutation, suggesting that it may represent an intermediate form in the evolution between these two subfamilies. Subsequently, we developed a PCR-based assay to detect the polymorphism, rendering it a more useful marker for genetic linkage studies and genome mapping. This insertion is also a valuable polymorphism for human population studies, as demonstrated by the large variations in allele frequencies seen in three population groups.

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References

  • Antonarakis, S. E., P. Oettgen, A. Chrakravarti, S. L. Halloran, R. R. Hudson, L. Feisee & S. K. Karathanasis, 1988. DNA polymorphism haplotypes of the human apolioprotein APOA1-APOC3-APOA4 gene cluster. Hum. Genet. 80:265–273.

    PubMed  Google Scholar 

  • Ausabel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl, 1987. Current Protocols in Molecular Biology. Wiley, New York.

    Google Scholar 

  • Bailey, A. D. & C.-K. J. Shen, 1993. Sequential insertion of Alu family repeats into specific genomic sites of higher primates. Proc. Natl. Acad. Sci. USA 90:7205–7209.

    PubMed  Google Scholar 

  • Batzer, M. A., C. W. Schmid & P. L. Deininger, 1993. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol. 224: 213–232.

    PubMed  Google Scholar 

  • Batzer, M. A., M. Alegria-Hartman, H. Bazan, D. H. Kass, T. H. Shaikh, G. E. Novick, P. A. Ioannou, D. A. Boudreau, W. D. Scheer, R. J. Herrera, M. Stoneking & P. L. Deininger, 1993. Alu repeats as markers for human population genetics, pp. 49–57 in Proceedings from the 4th International Symposium on Human Identification. Promega Publishing.

  • Batzer, M. A. & P. L. Deininger, 1991. A human-specific subfamily of Alu sequence. Genomics 9:481–487.

    PubMed  Google Scholar 

  • Batzer, M. A., V. A. Gudi, J. C. Mena, D. W. Foltz, R. J. Herrera & P. L. Deininger, 1991. Amplification dynamics of human-specific (HS) Alu family members. Nucleic Acids Res. 19:3619–3623.

    PubMed  Google Scholar 

  • Batzer, M. A., G. E. Kilroy, P. E. Richard, T. H. Shaikh, T. D. Desselle, C. L. Hoppens & P. L. Deininger, 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18:6793–6798.

    PubMed  Google Scholar 

  • Board, P. G., G. C. Webb, J. McKee & A. Ichinose, 1988. Localization of the coagulation factor XIII A subunit gene (F13A) to chromosome bands6p24-25. Cytogenet. Cell Genet. 48:25–27.

    PubMed  Google Scholar 

  • Bottenus, R. E., A. Ichinose & E. W. Davie, 1990. Nucleotide sequence of the gene for the b subunit of human factor XIII. Biochemistry 29:11195–11209.

    PubMed  Google Scholar 

  • Britten, R. J., W. F. Baron, D. B. Stout & E. H. Davidson, 1988. Sources and evolution of human Alu repeated sequences. Proc. Natl. Acad. Sci. USA 85:4770–4774.

    PubMed  Google Scholar 

  • Cambien, F., O. Poirier, L. Lecerf, A. Evans, J.-P. Cambou, D. Arveiler, G. Luc, J.-M. Bard, L. Bara, R. Ricard, L. Tiret, P. Amouyel, F. Alhenc-Gelas & F. Soubrier, 1992. Deletion polymorphism in the gene for angiotensin-convering enzyme is a potent risk factor for myocardial infarction. Nature 359: 641–644.

    PubMed  Google Scholar 

  • Daniels, G. R. & P. L. Deininger, 1985. Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res. 13:8939–8954.

    PubMed  Google Scholar 

  • Deininger, P. L., 1989. SINEs, short interspersed repeated DNA elements in higher eucaryotes, pp. 619–636 in Mobile DNA edited by M. Howe & D. Berg. ASM Press, Washington, DC.

    Google Scholar 

  • Deininger, P. L. & M. A. Batzer, 1993. Evolution of retroposons, pp. 157–196 in Evolutionary Biology Vol. 27, edited by M./ K. Hecht, R. J. MacIntyre & M. T. Clegg. Plenum Press, New York.

    Google Scholar 

  • Deininger, P. L., M. A. Batzer, C. A. Hutchison III & M. H. Edgell, 1992. Master genes in mammalian repetitive DNA amplification. Trends Genet. 8:307–311.

    PubMed  Google Scholar 

  • Economou-Pachnis, A. & P. N. Tsichlis, 1985. Insertion of an Alu SINE in the human homologue of the MIvi-2 locus. Nucleic Acids Res. 13:8379–8387.

    PubMed  Google Scholar 

  • Edwards, M. C. & M. C. Gibbs, 1992. A human dimorphism resulting from loss of an Alu. Genomics 14:590–597.

    PubMed  Google Scholar 

  • Friezner-Degen, S. J., B. Rajput & E. Reich, 1986. The human tissue plasminogen activator gene. J. Biol. Chem. 261:6972–6985.

    PubMed  Google Scholar 

  • Goldberg, Y. P., J. M. Rommens, S. E. Andrew, G. B. Hutchinson, B. Lin, J. Theilmann, R. Graham, M. L. Glaves, E. Starr, H. McDonald, J. Nasir, K. Schappert, M. A. Kalchman, L. A. Clarke & M. R. Hayden, 1993. Identification of an Alu retrotransposition event in close proximity to a strong candidate gene for Huntington's disease. Nature 362:370–373.

    PubMed  Google Scholar 

  • Hutchinson, G. B., S. E. Andrew, H. McDonald, Y. P. Goldberg, R. Graham, J. M. Rommens & Rommens M. R. and Hayden, 1993. An Alu element retroposition in two families with Huntington disease defines a new active Alu subfamily. Nucleic Acids Res. 21: 3379–3383.

    PubMed  Google Scholar 

  • Jurka, J., 1993. A new subfamily of recently retroposed Alu-repeats. Nucleic Acids Res. 21:2252.

    PubMed  Google Scholar 

  • Jurka, J. & A. Milosavljevic, 1991. Reconstruction and analysis of human Alu genes. J. Mol. Evol. 32:105–121.

    PubMed  Google Scholar 

  • Jurka, J. & T. Smith, 1988. A fundamental division in the Alu family of repeated sequences. Proc. Natl. Acad. Sci. USA 85:4775–4778.

    PubMed  Google Scholar 

  • Matera, A. G., U. Hellmann, M. F. Hintz & C. W. Schmid, 1990. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 18:6019–6023.

    PubMed  Google Scholar 

  • Matera, A. G., U. Hellmann & C. W. Schmid, 1990. A transpositionally and transcriptionally competent Alu subfamily. Mol. Cell. Biol. 10:5424–5432.

    PubMed  Google Scholar 

  • Mietus-Snyder, M., P. Charmley, B. Korf, J. A. A. Ladias, R. A. Gatti & S. K. Karathanasis, 1990. Genetic linkage of the human apolipoprotein AI-CIII-AIV gene cluster and the neural cell adhesion molecule (NCAM) gene. Genomics 7:633–637.

    PubMed  Google Scholar 

  • Miyamoto, M. M., J. L. Slightom & M. Goodman, 1987. Phylogenetic relations of humans and African apes from DNA sequences in the ψN-globin region. Science 238:369–373.

    PubMed  Google Scholar 

  • Mizutani, K., H. Nishimukai, T. Yasugi, I. Iwahashi, K. Tsunekawa & T. Shinomiya, 1991. Polymorphisms of serum proteins in Japanese patients with vascular diseases. I. Factor XIIIB, plasminogen and complementtypes in primary varicose veins. Hum. Hered. 41:270–275.

    PubMed  Google Scholar 

  • Muratani, K., T. Hada, Y. Yamamoto, T. Kaneko, Y. Shigeto, T. Ohue, J. Furuyama & K. Higashino, 1991. Inactivation of the cholinesterase geen by Alu insertion: Possible mechanism for human gene transposition. Proc. Natl. Acad. Sci. USA 88: 11315–11319.

    PubMed  Google Scholar 

  • Nakamura, Y., M. Leppert, P. O'Connell, R. Wolff, T. Holm, M. Culver, C. Martin, E. Fujimoto, M. Hoff, E. Kumlin & R. White, 1987. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235:1616–1622.

    PubMed  Google Scholar 

  • Perna, N. T., M. A. Batzer, P. L. Deininger & M. Stoneking, 1992. Alu insertion polymorphism: A new type of marker for human population studies. Hum. Biol. 64:641–648.

    PubMed  Google Scholar 

  • Quentin, Y., 1988. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J. Mol. Evol. 27:194–202.

    PubMed  Google Scholar 

  • Ryan, S. C. & A. Dugaiczyk, 1989. Newly arisen DNA repeats in primate phylogeny. Proc. Natl. Acad. Sci. USA 86:9360–9364.

    PubMed  Google Scholar 

  • Sanger, F., S. Nicklen & A. R. Coulson, 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463–5467.

    PubMed  Google Scholar 

  • Sawada, I. & C. W. Schmid, 1986. Primate evolution of the α-globin gene cluster and its Alu-like repeats. J. Mol. Biol. 192:693–703.

    PubMed  Google Scholar 

  • Sawada, I., C. Willard, C.-K. J. Shen, B. Chapman, A. C. Wilson & C. W. Schmid, 1985. Evolution of Alu family repeats since the divergence of human chimpanzee. J. Mol. Evol. 22:316–322.

    PubMed  Google Scholar 

  • Schwartz, M. L., V. P. Salvatore, R. L. Hill & P. A. MacKee, 1973. Human factor XIII from plasma and platelets. J. Biol. Chem. 246:5851–5854.

    Google Scholar 

  • Shen, M. R., M. A. Batzer & P. L. Deininger, 1991. Evolution of the master Alu gene(s). J. Mol. Evol. 33:311–320.

    PubMed  Google Scholar 

  • Slagel, V. & P. L. Deininger, 1989. In vivo transcription of a cloned prosimian SINE sequence. Nucleic Acids Res. 17:8669–8682.

    PubMed  Google Scholar 

  • Slagel, V., E. Flemington, V. Traina-Dorge, H. Bradshaw & P. L. Deininger, 1987. Clustering and subfamily relationships of the Alu family in the human genome. Mol. Biol. Evol. 4:19–29.

    PubMed  Google Scholar 

  • Stoppa-Lyonnet, D., P. E. Carter, T. Meo & M. Tosi, 1990. Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc. Natl. Acad. Sci. USA 87:1551–1557.

    PubMed  Google Scholar 

  • Tiret, L., B. Riget, S. Visvikis, C. Breda, P. Corvol, F. Cambien & F. Soubrier, 1992. Evidence from combined segregation and linkage analysis, that a variant of the angiotensin I-converting enzyme (ACE) gene controls plasma ACE levels. Am. J. Hum. Genet. 51:197–205.

    PubMed  Google Scholar 

  • Vidaud, D., M. Vidaud, B. R. Bahnak, V. Siguret, S. G. Sanchez, Y. Laurin, D. Meyer, M. Goossens & J. M. Lavergne, 1993. Hemophilia B due to a de novo insertion of a human-specific Alu subfamily member within the coding region of the factor IX gene. Eur. J. Hum. Genet. 1:30–36.

    PubMed  Google Scholar 

  • Wallace, M. R., L. B. Anderson, A. M. Saulino, P. E. Gregory, T. W. Glover & F. S. Collins, 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353:864–866.

    PubMed  Google Scholar 

  • Webb, G. C., M. Coggan, A. Ichinose & P. G. Board, 1989. Localization of the coagulation factor XIII B subunit gene (F13B) to chromosome bands 1q31-32.1 and restriction fragment length polymorphism at the locus. Hum. Genet. 81:157–160.

    PubMed  Google Scholar 

  • Weber, J. L. & P. E. May, 1989. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44:388–396.

    PubMed  Google Scholar 

  • Weiner, A. M., P. L. Deininger & A. Efstratiadis, 1986. Nonviral retroposons: Genes, pseudogenes and transposable elements generated by the reverse flow of genetic information. Ann. Rev. Biochem. 55:631–661.

    PubMed  Google Scholar 

  • Willard, C., H. T. Nguyen & C. W. Schmid, 1987. Existence of at least three distinct Alu subfamilies. J. Mol. Evol. 26:180–186.

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, 1901 Perdido St., 70112, New Orleans, LA, USA

    David H. Kass, Claudina Aleman & Prescott L. Deininger

  2. Human Genome Center, L-452, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, P.O. Box 808, 94551, Livermore, CA, USA

    Mark A. Batzer

  3. Laboratory of Molecular Genetics, Alton Ochsner Medical Foundation, 70121, New Orleans, LA, USA

    Prescott L. Deininger

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  1. David H. Kass
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  2. Claudina Aleman
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  4. Prescott L. Deininger
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Kass, D.H., Aleman, C., Batzer, M.A. et al. Identification of a human specificAlu insertion in the factor XIIIB gene. Genetica 94, 1–8 (1994). https://doi.org/10.1007/BF01429214

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