The multiple origins of human Alu sequences (original) (raw)
Abarbanel RM, Wieneke PR, Mansfield E, Jaffe DA, Brutlag DL (1984) Rapid searches for complex patterns in biological molecules. Nucleic Acids Res 12:263–280 PubMed Google Scholar
Bains W (1986) MULTAN: a program to align multiple DNA sequences. Nucleic Acids Res 14:159–177 PubMed Google Scholar
Barrie PA, Jeffreys AJ, Scott AF (1981) Evolution of the β-globin genes cluster in man and primates. J Mol Biol 149:319–336 ArticlePubMed Google Scholar
Bell B, Pictet R, Rutter WJ (1980) Analysis of the regions flanking the human insulin gene and sequence of an Alu family member. Nucleic Acids Res 8:4091–4109 PubMed Google Scholar
Bennet K, Hill RE, Pietras DF, Woodsworth-Gutai M, Kane-Haas C, Houston JM, Health JK, Hastie, ND (1984) Most highly repeated dispersed DNA families in the mouse genome. Mol Cell Biol 4:1561–1571 PubMed Google Scholar
Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499–1504 PubMed Google Scholar
Brown AL (1984) On the origin of the Alu family of repeated sequences. Nature 312:106 ArticlePubMed Google Scholar
Brownell E, Krystal M, Arnheim N (1983) Structure and evolution of human and African ape rDNA pseudogenes. Mol Biol Evol 1:29–37 PubMed Google Scholar
Chang L-YE, Slightom JL (1984) Isolation and nucleotide sequence of the beta-type globin pseudogene from human, gorilla and chimpanzee. J Mol Biol 180:767–784 ArticlePubMed Google Scholar
Chung DW, Que BG, Rixon MW, Mace M Jr, Davie EW (1983) Characterisation of complementary deoxyribonucleic acid and genomic DNA for the beta chain of human fibrinogen. Biochemistry 22:3244–3250 ArticlePubMed Google Scholar
Clayton J, Kedes L (1982) GEL, a DNA sequencing project management system. Nucleic Acids Res 10:305–321 PubMed Google Scholar
Colby WW, Chen EY, Smith DH, Levinson AD (1983) Identification and nucleotide sequence of a human locus homologous to the v-myc oncogene of avian myelocytomatosis virus MC29. Nature 301:722–725 ArticlePubMed Google Scholar
Comb M, Rosen H, Seeburg P, Adelman J, Herbert E (1983) Primary structure of the human proenkephalin gene. DNA 2:213–229 PubMed Google Scholar
Daniels GR, Deininger PL (1985) Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res 13:8939–8954 PubMed Google Scholar
Daniels GR, Fox GM, Loewensteiner D, Schmid CW, Deininger PL (1983) Species-specific homogeneity of the primate Alu family of repeated DNA sequences. Nucleic Acids Res 11:7579–7593 PubMed Google Scholar
Das HK, Lawrance SK, Weissman SM (1983) Structure and nucleotide sequence of the heavy chain gene of HLA-DR. Proc Natl Acad Sci USA 80:3543–3547 PubMed Google Scholar
Davidson EH, Graham DE, Neufeld BR, Chamberlin ME, Amenson CS, Hough BR, Britten RJ (1973) Arrangement and characterisation of repetitive sequence elements in animal DNAs. Cold Spring Harbor Symp Quant Biol 38:295–301 Google Scholar
Deininger PL, Jolly DJ, Rubin CM, Friedman T, Schmid CW (1981) Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J Mol Biol 151:17–33 ArticlePubMed Google Scholar
Di Segni G, Carrara G, Tocchini-Valentini GR, Shoulders CC, Baralle FE (1981) Selective in vitro transcription of one of the two Alu family repeats present in the 5′ flanking region of the human epsilon-globin gene. Nucleic Acids Res 9:6709–6722 PubMed Google Scholar
Dover GA (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117 ArticlePubMed Google Scholar
Duncan CH, Jagadeeswaran P, Wang RRC, Weissman SM (1981) Structural analysis of templates and RNA polymerase III transcripts of Alu family sequences interspersed among the human beta-like globin genes. Gene 13:185–196 ArticlePubMed Google Scholar
Economou-Pachis A, Tsichlis PN (1985) Insertation of an Alu SINE in the human homologue of the Mliv-2 locus. Nucleic Acids Res 13:5073–5091 Google Scholar
Farris (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668 Article Google Scholar
Friezner Degen SJ, MacGillivray RTA, Davie DW (1983) Characterization of the complementary deoxyribonucleic acid and gene coding for human prothrombin. Biochemistry 22:2087–2097 ArticlePubMed Google Scholar
Frommer M, Prosser J, Vincent PC (1984) Human satellite I sequences include a male-specific 2.47kb tandemly repeated unit containing one Alu family member per repeat. Nucleic Acids Res 12:2887–2900 PubMed Google Scholar
Fukuyami Y, Collins F, Kole R, Stoeckert CJ, Jagadeeswaran P, Duncan CH, Weissman SM (1983) Sequences of human repetitive DNA, alpha globin and MHC locus genes. I. Repeated sequence DNA. Cold Spring Harbor Symp Quant Biol 47:1079–1081 PubMed Google Scholar
Goodman M, Koop BF, Czelusniak J, Weiss ML, Slightom JL (1984) The_eta_-globin gene. Its long evolutionary history in the mammals. J Mol Biol 180:803–824 Google Scholar
Greenberg BH, Bencen GH, Seilhamer JJ, Lewicki JA, Fiddes JC (1984) Nucleotide sequence of the gene encoding human natriuetic factor precursor. Nature 312:656–658 ArticlePubMed Google Scholar
Grimaldi G, Singer MF (1983) Members of the KpnI family of long interspersed repeated sequences join and interrupt alphasatellite in the monkey genome. Nucleic Acids Res 11:321–338 PubMed Google Scholar
Hammarstrom K, Westin G, Bark C, Zarielski J, Peterson U (1984) Genes and pseudogenes for human U2 RNA. J Mol Biol 179:157–169 ArticlePubMed Google Scholar
Harris S, Barrie PA, Weiss ML, Jeffreys AJ (1984) The primate pseudo-beta-1 gene. An ancient beta-globin pseudogene. J Mol Biol 180:785–802 Google Scholar
Hess JF, Fox M, Schmid C, Shen C-KJ (1983) Molecular evolution of the human adult alpha-globin-like region: insertion and deletion of Alu family repeats and non-Alu DNA sequences. Proc Natl Acad Sci USA 80:5970–5975 PubMed Google Scholar
Houck CM, Rinehart FP, Schmid CW (1979) Ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 132:289–306 ArticlePubMed Google Scholar
Ito R, Sato K, Helmer T, Jay G, Agarwal K (1984) Structural analysis of the gene encoding human gastrin: The large intron contains an Alu sequence. Proc Natl Acad Sci USA 81:4662–4666 PubMed Google Scholar
Jagadeeswaran P, Forget BG, Weissman SM (1981) Short interspersed repetitive DNA elements in eukaryotes: transposable DNA elements generated by reverse transcrption of RNA Pol III transcipts? Cell 26:141–142 ArticlePubMed Google Scholar
Jeffreys AJ, Wilson V, Thein SL (1985) Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–73 ArticlePubMed Google Scholar
Jelinek WR, Toomey TP, Leinward L, Ducan CH, Biro PA, Choudry PV, Weissman SM, Rubin CM, Houck CM, Deininger PL, Schmid CW (1980) Ubiquitous interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci USA 77:1398–1402 PubMed Google Scholar
Jukes TH, Cantor CR (1969) In: Munro HN (ed) Mammalian protein metabolism III. Academic, New York, pp 21–132 Google Scholar
Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458 PubMed Google Scholar
Krayev AS, Markusheva TV, Kramerov DA, Ryskov AP, Skryabin KG, Bayev AA, Georgiev GP (1982) Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B1 sequencing. Nucleic Acids Res 10:7461–7475 PubMed Google Scholar
Lee MG-S, Lewis SA, Wilde CD, Cowan NJ (1983) Evolutionary history of a multigene family: an expressed human beta-tubulin gene and three processed pseudogenes. Cell 33:477–487 ArticlePubMed Google Scholar
Lee MG-S, Loomis C, Cowan NJ (1984) Sequence of an expressed human beta-tubulin gene containing ten Alu family members. Nucleic Acids Res 12:5823–5836 PubMed Google Scholar
Maeda N, Bliska JB, Smithies O (1983) Recombination and balanced chromosome polymorphism suggested by DNA sequences 5′ to the human δ-globin gene. Proc Natl Acad Sci USA 80:5012–5016 PubMed Google Scholar
Martin SL, Vincent KA, Wilson AC (1983) Rise and fall of the delta globin gene. J Mol Biol 164:513–528 ArticlePubMed Google Scholar
Miyada T, Hayashida H (1981) Extraordinarily high evolutionary rate of pseudogenes: evidence of the presence of selective pressure against changes between synonymous codons. Proc Natl Acad Sci 78:5739–5743 PubMed Google Scholar
Miyake T, Migita K, Sakaki Y (1983) Some KpnI family members are associated with the Alu family in the human genome. Nucleic Acids Res 11:6837–6846 PubMed Google Scholar
Murphy S, Altruda F, Ullu E, Tripodi M, Silengo L, Melli M (1984) DNA sequences complementary to human 7SK RNA show structural similarities to the short mobile elements of the mammalian genome. J Mol Biol 177:575–590 ArticlePubMed Google Scholar
Myers JC, Dickson LA, de Wet WJ, Bernard MP, Chu M-L, Di Liberto M, Pepe G, Sangiorgi FO, Ramirez F (1983) Analysis of the 3′ end of the human pro-alpha-2(I) collagen gene. J Biol Chem 258:10128–10135 PubMed Google Scholar
Nemer M, Chamberland M, Sirois D, Argentin S, Drouin J, Dixon RAF, Zivin RA, Condra JH (1984) Gene structure of human cardiac hormone precursor, pronatriodilatin. Nature 312:654–656 ArticlePubMed Google Scholar
Ohta T, Dover GA (1984) The cohesive population genetics of molecular drive. Genetics 108:501–521 PubMed Google Scholar
Pan J, Elder JT, Duncan CH, Weissman SM (1981) Structural analysis of interspersed repetitive polymerase III transcription units in human DNA. Nucleic Acids Res 9:1151–1170 PubMed Google Scholar
Perez-Stable C, Ayres TM, Shen C-KJ (1984) Distinctive sequence organisation and functional programming of an Alu repeat promoter. Proc Natl Acad Sci USA 81:5291–5295 PubMed Google Scholar
Sawada I, Beal MP, Shen C-KJ, Chapman B, Wilson AC, Schmid C (1983) Intergenic DNA sequences flanking the pseudo alpha globin genes of human and chimpanzee. Nucleic Acids Res 11:8087–8101 PubMed Google Scholar
Sawada I, Willard C, Shen C-KJ, Chapman B, Wilson AC, Schmid CW (1985) Evolution of Alu family repeats since the divergence of human and chimpanzee. J Mol Evol 22:316–322 PubMed Google Scholar
Schmid CW, Jelinek WR (1982) The Alu family of dispersed repetitive sequences. Science 216:1065–1070 PubMed Google Scholar
Seeburg PH (1982) The growth hormone gene family: Nucleotide sequences show recent divergence and predict a new polypeptide hormone. DNA 1:239–249 PubMed Google Scholar
Sharp PA (1983) Conversion of RNA to DNA in mammals: Alu-like elements and pseudogenes. Nature 301:471–472 ArticlePubMed Google Scholar
Shimada T, Chen M-J, Nienhuis AW (1984) A human dihydrofolate reductase intronless pseudogene with an Alu repetitive sequence: multiple insertions at a single chromosomal site. Gene 31:1–8 ArticlePubMed Google Scholar
Tajima F (1983) Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437–460 PubMed Google Scholar
Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138 PubMed Google Scholar
Tsukada T, Watanabe Y, Nakai Y, Imura H, Nakanashi S, Numa S (1983) Repetitive DNA sequences in the human corticotropin-β-lipotropin precursor gene region: Alu family members. Nucleic Acids Res 10:1471–1479 Google Scholar
Ullu E, Tschudi C (1984) Alu sequences are processed 7SL RNA genes. Nature 312:171–172 PubMed Google Scholar
Wilbur WJ, Lipman DJ (1983) Rapid similarity searches of nucleic acid and protein data bases. Proc Natl Acad Sci USA 80:726–730 Google Scholar
Willard C, Wong E, Hess JF, Shen C-KJ, Chapman B, Wilson AC, Schmid CW (1985) Comparison of human and chimpanzee zeta-1 globin genes. J Mol Evol 22:309–315 PubMed Google Scholar
Yamamoto T, Davis CG, Brown MS, Schneider WJ, Casey ML, Goldstein JL, Russell DW (1984) The human LDL receptor: a cysteine-rich protein with multiple Alu sequences in its mRNA. Cell 39:27–38 ArticlePubMed Google Scholar
Yang R, Fristensky B, Deutch AH, Huang R-CC, Tan YH, Narang SA, Wu R (1983) The nucleotide sequence of a new human repetitive DNA consists of eight tandem repeats of 66 base pairs. Gene 25:59–66 ArticlePubMed Google Scholar