Abstract
Alu elements are a class of repetitive DNA sequences found throughout the human genome that are thought to be duplicated via an RNA intermediate in a process termed retroposition. Recently inserted Alu elements are closely related, suggesting that they are derived from a single source gene or closely related source genes. Analysis of the type III collagen gene (COL3A1) revealed a polymorphic Alu insertion in intron 8 of the gene. The Alu insertion in the COL3A1 gene had a high degree of nucleotide identity to the Sb family of Alu elements, a family of older Alu elements. The Alu sequence was less similar to the consensus sequence for the PV or Sb2 subfamilies, subfamilies of recently inserted Alu elements. These data support the observations that at least three source genes are active in the human genome, one of which is distinct from the PV and Sb2 subfamilies and predates either of these two subfamilies. Appearance of the Alu insertion in different ethnic populations suggests that the insertion may have occurred in the last 100,000 years. This Alu insert should be a useful marker for population studies and for marking COL3A1 alleles.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Adams MD, Kerlavage AR, Fields C, Venter JC (1993) 3400 expressed sequence tages identify diversity of transcripts from human brain. Nature Genet 4:256–267
Batzer MA, Deininger PL (1991) A human-specific subfamily of Alu sequences. Genomics 9:481–487
Batzer MA, Stoneking M, Alegria-Hartmen M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ, Deninger PL (1994) African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci USA 91:12288–12292
Benson-Chanda V, Su MW, Weil D, Chu ML, Ramirez F (1989) Cloning and analysis of the 5′ portion of the human type III procollagen gene (COL3A1). Gene 78:255–265
Blonden LAJ, Terwindt GM, Den Dunnem JT, Van Ommen G-JB (1994) A polymorphic STS in intron 44 of the dystrophin gene. Hum Genet 93:479–480
Britten RJ, Baron WF, Stout DB, Davidson EH (1988) Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci USA 85:4770–4774
Britten RJ, Stout DB, Davidson EH (1989) The current source of human Alu retroposons is a conserved gene shared with old world monkey. Proc Natl Acad Sci USA 86:3718–3722
Cavalli-Sforza LL, Piazza A, Mountain J (1988) Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data. Proc Natl Acad Sci USA 85:6002–6006
Cavalli-Sforza LL (1991) Genes, peoples and languages. Sci Am 265:104–110
Deininger PL, Slagel VK (1988) Recently amplified Alu family members share a common parental Alu sequence. Mol Cell Biol 8:4566–4569
Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395
Economou-Pachnis A, Tsichlis NT (1985) Insertion of an Alu SINE in the human homologue of the MIvi-2 locus. Nucleic Acids Res 13:8379–8387
Higgins DG, Bleasby AJ, Fuchs R (1992) Clustal V improved software for multiple sequence alignment. CABIOS 8:189–191
Hutchinson G, Andrew S, McDonald H, Goldberg P, Graham J, Rommens J, Hayden MR (1993) AnAlu element retroposition in two families with Huntington disease defines a new activeAlu subfamily. Nucleic Acids Res 21:3379–3383
Jurka J (1993) A new subfamily of recently retroposed human Alu repeats. Nucleic Acids Res 21:2252
Jurka J (1995) Origin and evolution of Alu repetitive elements. In: Maraia RJ, Landes RG (eds) The impact of short interspersed elements. R.G. Landes Company, pp 25–41
Jurka J, Milosavljevic A (1991) Reconstruction and analysis of human Alu genes. J Mol Evol 32:105–121
Jurka J, Smith T (1988) A fundamental division in theAlu family of repeated sequences. Proc Natl Acad Sci USA 85:4775–4778
Lautner-Rieske A, Huber C, Meindl A, et al. (1992) The human immunoglobulin K locus. Characterization of the duplicated A regions. Eur J Immunol 22:1023–1029
Leeflang EP, Liu W-M, Hashimoto C, Choudary PV, Schmid CW (1992) Phylogenetic evidence for multiple Alu source genes. J Mol Evol 35:7–16
Ludwig M, Wohn KD, Schleuning WD, Olek K (1992) Allelic dimorphism in the human tissue-type plasminogen activator (TPA) gene as a result of an Alu insertion/deletion event. Hum Genet 88:388–392
Matera AG, Hellmann U, Schmid CW (1990a) A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol 10:5424–5431
Matera AG, Hellmann U, Hintz MF, Schmid CW (1990b) Recently transposed Alu repeats result from multiple source gene. Nucleic Acids Res 18:6019–6023
Merritt CM, Easteal S, Board PG (1990) Evolution of human alpha-acid glycoprotein genes and surrounding Alu repeats. Genomics 6:659–665
Mountain JL, Lin AA, Bowcock AM, Cavalli-Sforza LL (1992) Evolution of modern humans: evidence from nuclear DNA polymorphisms. Phil Trans R Soc Lond [Biol] 337:159–165
Muratani K, Toshikazu H, Yamamoto Y, Kaneko T, Shegeto Y, Ohue T, Furuyama J, Higashing K (1991) Inactivation of the cholinesterase gene byAlu insertion: possible mechanism for human gene transposition. Proc Nat Acad Sci USA 88:11315–11319
Quentin Y (1988) The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol 27:194–202
Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9:945–967
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Schmid C, Maraia R (1992) Transcriptional regulation and transposition selection of active SINE sequences. Current Opin Genet Dev 2:874–882
Schmid CW (1993) How many source Alus? Trends Genet 9:39
Shen MR, Batzer MA, Deininger PL (1991) Evolution of the master Alu gene(s). J Mol Evol 33:311–320
Slagel V, Flemington E, Traina-Dorge V, Bradshaw H, Deininger PL (1987) Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol 4:19–29
Stoppa-Lyonnet D, Carter PE, Meo T, Tosi M (1990) Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc Natl Acad Sci USA 87:1551–1555
Superti-Furga A, Steinmann B, Ramirez F, Byers PH (1989) Molecular defects of type III procollagen in Ehlers-Danlos syndrome type IV. Hum Genet 82:104–108
Trabuchet G, Chebloune Y, Savatier P, Lachuer J, Faure C, Verdier G, Nigon VM (1987) Recent insertion of an Alu sequence in the beta globulin gene cluster of the gorilla. J Mol Evol 25:288–291
Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, Collins FS (1991) Ade novo Alu insertion results in neurofibromatosis type 1. Nature 353:864–866
Willard C, Nguyen HT, Schmid CW (1987) Existence of at least three distinct Alu subfamilies. J Mol Evol 26:180–186
Zuckerkandl E, Latter G, Jurka J (1989) Maintenance of function without selection: Alu sequences as “cheap genes.” J Mol Evol 29:504–512
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Milewicz, D.M., Byers, P.H., Reveille, J. et al. A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific. J Mol Evol 42, 117–123 (1996). https://doi.org/10.1007/BF02198836
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF02198836