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Genetica

, Volume 107, Issue 1–3, pp 209–238 | Cite as

Genomes were forged by massive bombardments with retroelements and retrosequences

  • Jürgen Brosius
Article

Abstract

Retroposition is an efficient route to move coding regions around the genome ‘in search’ of novel regulatory elements and to shotgun regulatory elements into the genome ‘in search’ of new target genes. The templates for such retrogenes are mRNAs, and for regulatory retronuons (nuon=any definable nucleic acid sequence) usually small non-mRNAs. An example in support of the ‘master gene’ model for SINEs (short interspersed repetive elements) is provided with neuronal BC1 RNA. Furthermore, an alternative explanation of LINE (long interspersed repetive elements) involvement in the generation of SINEs is given. I will also argue that the status of transposable elements with respect to the host resembles more symbiosis than parasitiasis and that host defense is often lenient as if even to ‘tolerate or support’ retronuons. Finally the paradox of evolution's lack of foresight and the future exaptive use of retronuons is being dealt with by referring to W.F. Doolittle's ‘Hierarchical Approaches to Genome Evolution’.

evolution genomic symbionts host defense impact on genomes retronuons reverse transcription template switching 

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Table references

  1. Adra, C.N., N.A. Ellis & M.W. McBurney, 1988. The family of mouse phosphoglycerate kinase genes and pseudogenes. Somat. Cell. Mol. Genet. 14: 69–81.PubMedGoogle Scholar
  2. Akira, S., H. Isshiki, T. Sugita, O. Tanabe, S. Kinoshita, Y. Nishio, T. Nakajima, T. Hirano & T. Kishimoto, 1990. A nuclear factor for IL-6 expression (NF-IL6) is a member of a C/EBP family. Embo J. 9: 1897–1906.PubMedGoogle Scholar
  3. Almenoff, J.S., J. Jurka & O.K. Schoolnik, 1994. Induction of heatstable enterotoxin receptor activity by a human Alu repeat. J. Biol. Chem. 269: 16610–16617.PubMedGoogle Scholar
  4. Alvarez-Bolado, G., M.G. Rosenfeld & L.W. Swanson, 1995. Model of forebrain regionalization based on spatiotemporal patterns of POU-III homeobox gene expression, birthdates, and morphological features. J. Comp. Neurol. 355: 237–295.PubMedGoogle Scholar
  5. Andersen, R.D., B.W. Birren, S.J. Taplitz & H.R. Herschman, 1986. Rat metallothionein-1 structural gene and three pseudogenes, one of which contains 5′-regulatory sequences. Mol. Cell. Biol. 6: 302–314.PubMedGoogle Scholar
  6. Andrea, J.E. & M.P. Walsh, 1995. Identification of a brain-specific protein kinase C zeta pseudogene (psi PKC zeta) transcript. Biochem. J. 310: 835–843.PubMedGoogle Scholar
  7. Aronow, B.J., R.N. Silbiger, M.R. Dusing, J.L. Stock, K.L. Yager, S.S. Potter, J.J. Hutton & D.A. Wiginton, 1992. Functional analysis of the human adenosine deaminase gene thymic regulatory region and its ability to generate position-independent transgene expression. Mol. Cell. Biol. 12: 4170–4185.PubMedGoogle Scholar
  8. Arranz, V., M. Kress & M. Ernoult-Lange, 1994. The gene encoding the MOK-2 zinc-finger protein: characterization of its promoter and negative regulation by mouse Alu type-2 repetitive elements. Gene 149: 293–298.PubMedGoogle Scholar
  9. Ashworth, A., B. Skene, S. Swift & B.R. Lovell, 1990. Zfa is an expressed retroposon derived from an alternative transcript of the Zfx gene. Embo J. 9: 1529–1534.PubMedGoogle Scholar
  10. Atanasoski, S., S.S. Toldo, U. Malipiero, E. Schreiber, R. Fries & A. Fontana, 1995. Isolation of the human genomic brain-2/N-Oct 3 gene (POUF3) and assignment to chromosome 6q16. Genomics 26: 272–280.PubMedGoogle Scholar
  11. Baniahmad, A., M. Muller, C. Steiner & R. Renkawitz, 1987. Activity of two different silencer elements of the chicken lysozyme gene can be compensated by enhancer elements. Embo J. 6: 2297–2303.PubMedGoogle Scholar
  12. Banki, K., D. Halladay & A. Perl, 1994. Cloning and expression of the human gene for transaldolase. A novel highly repetitive element constitutes an integral part of the coding sequence. J. Biol. Chem. 269: 2847–2851.PubMedGoogle Scholar
  13. Banville, D. & Y. Boie, 1989. Retroviral long terminal repeat is the promoter of the gene encoding the tumor-associated calcium-binding protein oncomodulin in the rat. J. Mol. Biol. 207: 481–490.PubMedGoogle Scholar
  14. Bard, J.A., S.P. Nawoschik, B.F. O'Dowd, S.R. George, T.A. Branchek & R.L. Weinshank, 1995. The human serotonin 5-hydroxytryptamine 1D receptor pseudogene is transcribed. Gene 153: 295–296.PubMedGoogle Scholar
  15. Barnes, D.E., G. Stamp, I. Rosewell, A. Denzel & T. Lindahl, 1998. Targeted disruption of the gene encoding DNA ligase IV leads to lethality in embryonic mice. Curr Biol. 8: 1395–1398.PubMedGoogle Scholar
  16. Baumruker, T., C. Gehe & I. Horak, 1988. Insertion of a retro-transposon within the 3′ end of a mouse gene provides a new functional polyadenylation signal. Nucleic Acids Res. 16: 7241–7251.PubMedGoogle Scholar
  17. Bejarano, L.A. & M.M. Valdivia, 1996. Molecular cloning of an intronless gene for the hamster centromere antigen CENP-B. Biochim Biophys Acta. 1307: 21–25.PubMedGoogle Scholar
  18. Berchtold, M.W., M. Koller, R. Egli, J.A. Rhyner, H. Hameister & E.E. Strehler, 1993. Localization of the intronless gene coding for calmodulin-like protein CLP to human chromosome 10p 13-ter. Hum Genet. 90: 496–500.PubMedGoogle Scholar
  19. Berquin, I.M., M. Ahram & B.F. Sloane, 1997. Exon 2 of human cathepsin B derives from an Alu element. FEBS Lett. 419: 121–123.PubMedGoogle Scholar
  20. Berry, G.T., J.J. Mallee, H.M. Kwon, J.S. Rim, W.R. Mulla, M. Muenke & N.B. Spinner, 1995. The human osmoregulatory Na+/myo-inositol cotransporter gene (SLC5A3): molecular cloning and localization to chromosome 21. Genomics 25: 507–513.PubMedGoogle Scholar
  21. Bhandari, B., W.J. Roesler, K.D. DeLisio, D.J. Klemm, N.S. Ross & R.E. Miller, 1991. A functional promoter flanks an intronless glutamine synthetase gene. J. Biol. Chem. 266: 7784–7792.PubMedGoogle Scholar
  22. Bi, S., O. Gavrilova, D.W. Gong, M.M. Mason & M. Reitman, 1997. Identification of a placental enhancer for the human leptin gene. J. Biol. Chem. 272: 30583–30588.PubMedGoogle Scholar
  23. Bignon, C., M. Roux-Dosseto, M.E. Zeigler, M.S. Wicha & P.M. Martin, 1992. cDNA cloning and genomic analysis of a new multigene family sharing common phylogenetic and expression profiles with the laminin receptor gene. Biochem. Biophys. Res. Commun. 184: 1165–1172.PubMedGoogle Scholar
  24. Blackshear, P.J., J.S. Tuttle, R.J. Oakey, M.F. Seldin, M. Chery, C. Philippe & D.J. Stumpo, 1992. Chromosomal mapping of the human (MACS) and mouse (Macs) genes encoding the MARCKS protein. Genomics 14: 168–174.PubMedGoogle Scholar
  25. Blum, M., D.M. Grant, W. McBride, M. Heim & U.A. Meyer, 1990a. Human arylamine N-acetyltransferase genes: isolation, chromosomal localization, and functional expression. DNA Cell. Biol. 9: 193–203.PubMedGoogle Scholar
  26. Blum, M., M. Heim & U.A. Meyer, 1990b. Nucleotide sequence of rabbit NAT1 encoding monomorphic arylamine Nacetyltransferase. Nucleic Acids Res. 18: 5287.PubMedGoogle Scholar
  27. Blum, M., M. Heim, & U.A. Meyer, 1990c. Nucleotide sequence of rabbit NAT2 encoding polymorphic liver arylamine N-acetyltransferase (NAT). Nucleic Acids Res. 18: 5295.PubMedGoogle Scholar
  28. Boccaccio, I., H. Glatt-Deeley, F. Watrin, N. Ro# ckel, M. Lalande & F. Muscatelli, 1999. The human MAGEL2 gene and its mouse homologue are paternally expressed and mapped to the Prader-Willi region. Hum. Mol. Genet. 8: 2497–2505.PubMedGoogle Scholar
  29. Boer, P.H., C.N. Adra, Y.F. Lau & M.W. McBurney, 1987. The testis-specific phosphoglycerate kinase gene pgk-2 is a recruited retroposon. Mol. Cell. Biol. 7: 3107–3112.PubMedGoogle Scholar
  30. Boggaram, V., K. Qing & C.R. Mendelson, 1988. The major apoprotein of rabbit pulmonary surfactant. Elucidation of primary sequence and cyclic AMP and developmental regulation. J. Biol. Chem. 263: 2939–2947.PubMedGoogle Scholar
  31. Bozza, M., L.F. Kolakowski, Jr., N.A. Jenkins, D.J. Gilbert, N.G. Copeland, J.R. David & C. Gerard, 1995. Structural characterization and chromosomal location of the mouse macrophage migration inhibitory factor gene and pseudogenes. Genomics 27: 412–419.PubMedGoogle Scholar
  32. Brini, A.T., G.M. Lee & J.P. Kinet, 1993. Involvement of Alu sequences in the cell-specific regulation of transcription of the gamma chain of Fc and T cell receptors. J. Biol. Chem. 268: 1355–1361.PubMedGoogle Scholar
  33. Brosius, J., 1999. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet. 15: 304–305.PubMedGoogle Scholar
  34. Brunovskis, P. & H.J. Kung, 1996. Retrotransposition and herpesvirus evolution. Virus Genes. 11: 259–270.Google Scholar
  35. Cao, Z., R.M. Umek & S.L. McKnight, 1991. Regulated expression of three C/EBP isoforms during adipose conversion of 3T3-L1 cells. Genes Dev. 5: 1538–1552.PubMedGoogle Scholar
  36. Carsana, A., E. Confalone, M. Palmieri, M. Libonati & A. Furia, 1988. Structure of the bovine pancreatic ribonuclease gene: the unique intervening sequence in the 5′ untranslated region contains a promoter-like element. Nucleic Acids Res. 16: 5491–5502.PubMedGoogle Scholar
  37. Chadwick, B.P., J. Mull, L.A. Helbling, S. Gill, M. Leyne, C.M. Robbins, H.W. Pinkett, I. Makalowska, C. Maayan, A. Blumenfeld, F.B. Axelrod, M. Brownstein, J.F. Gusella & S.A. Slaugenhaupt, 1999. Cloning, mapping, and expression of two novel actin genes, actin-like-7A (ACTL7A) and actin-like-7B (ACTL7B), from the familial dysautonomia candidate region on 9q31. Genomics 58: 302–309.PubMedGoogle Scholar
  38. Chakrabarti, R., R.B. McCracken, Jr., D. Chakrabarti & W.W. Souba, 1995. Detection of a functional promoter/enhancer in an intron-less human gene encoding a glutamine synthetase-like enzyme. Gene 153: 163–199.PubMedGoogle Scholar
  39. Chang, C.J., T.T. Chen, H.Y. Lei, D.S. Chen & S.C. Lee, 1990. Molecular cloning of a transcription factor, AGP/EBP, that belongs to members of the C/EBP family. Mol. Cell. Biol. 10: 6642–6653.PubMedGoogle Scholar
  40. Chang-Yeh, A., D.E. Mold & R.C. Huang, 1991. Identification of a novel murine IAP-promoted placenta-expressed gene. Nucl. Acids Res. 19: 3667–3672.PubMedGoogle Scholar
  41. Chen, A., H. Mannen & S.S. Li, 1998. Characterization of mouse ubiquitin-like SMT3A and SMT3B cDNAs and gene/pseudogenes. Biochem. Mol. Biol. Int. 46: 1161–1174.PubMedGoogle Scholar
  42. Chen, M.J., T. Shimada, A.D. Moulton, M. Harrison & A.W. Nienhuis, 1982. Intronless human dihydrofolate reductase genes are derived from processed RNA molecules. Proc. Natl. Acad. Sci. USA 79: 7435–7439.PubMedGoogle Scholar
  43. Chen, Y.T., W.J. Rettig, A.K. Yenamandra, C.A. Kozak, R.S. Chaganti, J.B. Posner & L.J. Old, 1990. Cerebellar degeneration-related antigen: a highly conserved neuroectodermal marker mapped to chromosomes X in human and mouse. Proc. Natl. Acad. Sci. USA 87: 3077–3081.PubMedGoogle Scholar
  44. Chiang, P.W., R. Zhang, L. Stubbs, L. Zhang, L. Zhu & D.M. Kurnit, 1998. Comparison of murine Supt4h and a nearly identical expressed, processed gene: evidence of sequence conservation through gene conversion extending into the untranslated regions. Nucleic Acids Res. 26: 4960–4964.PubMedGoogle Scholar
  45. Cho, K.O., B. Minsk & J.A. Wagner, 1990. NICER elements: a family of nerve growth factor-inducible cAMP-extinguishable retrovirus-like elements. Proc. Natl. Acad. Sci. USA 87: 3778–3782.PubMedGoogle Scholar
  46. Clemens, M.J. 1987. A potential role for RNA transcribed from B2 repeats in the regulation of mRNA stability. Cell 49: 157–158.PubMedGoogle Scholar
  47. Cole, S.E. & R.H. Reeves, 1998. A cluster of keratin-associated proteins on mouse chromosome 10 in the region of conserved linkage with human chromosome 21. Genomics 54: 437–442.PubMedGoogle Scholar
  48. Coy, J.F., S. Dubel, P. Kioschis, K. Thomas, G. Micklem, H. Delius & A. Poustka, 1996. Molecular cloning of tissue-specific transcripts of a transketolase-related gene: implications for the evolution of new vertebrate genes. Genomics 32: 309–316.PubMedGoogle Scholar
  49. Crowe, M.L., B.N. Perry & I.F. Connerton, 1996. Olfactory receptor-encoding genes and pseudogenes are expressed in humans. Gene 169: 247–249.PubMedGoogle Scholar
  50. Csoka, A.B., S.W. Scherer & R. Stern, 1999. Expression analysis of six paralogous human hyaluronidase genes clustered on chromosomes 3p21 and 7q31. Genomics 60: 356–361.PubMedGoogle Scholar
  51. Cyster, J., C. Somoza, N. Killeen & A.F. Williams, 1990. Protein sequence and gene structure for mouse leukosialin (CD43), a T lymphocyte mucin without introns in the coding sequence. Eur. J. Immunol. 20: 875–881.PubMedGoogle Scholar
  52. D'Onofrio, M., M.D. Lee, C.M. Starr, M. Miller & J.A. Hanover, 1991. The gene encoding rat nuclear pore glycoprotein p62 is intronless. J. Biol. Chem. 266: 11980–11985.PubMedGoogle Scholar
  53. Dahia, P.L., M.G. FitzGerald, X. Zhang, D.J. Marsh, Z. Zheng, T. Pietsch, A. von Deimling, F.G. Haluska, D.A. Haber & C. Eng, 1998. A highly conserved processed PTEN pseudogene is located on chromosome band 9p21. Oncogene 16: 2403–2406.PubMedGoogle Scholar
  54. Dahl, H.H., R.M. Brown, W.M. Hutchison, C. Maragos & G.K. Brown, 1990. A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded for by an intronless gene on chromosome 4. Genomics 8: 225–232.PubMedGoogle Scholar
  55. Danciger, E., C. Mettling, M. Vidal, R. Morris & F. Margolis, 1989. Olfactory marker protein gene: its structure and olfactory neuron-specific expression in transgenic mice. Proc. Natl. Acad. Sci. USA 86: 8565–8569.PubMedGoogle Scholar
  56. DeChiara, T.M. & J. Brosius, 1987. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc. Natl. Acad. Sci. USA 84: 2624–2628.PubMedGoogle Scholar
  57. Descombes, P., M. Chojkier, S. Lichtsteiner, E. Falvey & U. Schibler, 1990. LAP, a novel member of the C/EBP gene family, encodes a liver-enriched transcriptional activator protein. Genes Dev. 4: 1541–1551.PubMedGoogle Scholar
  58. Devilat, I. & P. Carvallo, 1993. Structure and sequence of an intron-less gene for human casein kinase II-alpha subunit. FEBS Lett. 316: 114–118.PubMedGoogle Scholar
  59. Devon, R.S., K.L. Evans, J.C. Maule, S. Christie, S. Anderson, J. Brown, Y. Shibasaki, D.J. Porteous & A.J. Brookes, 1997. Novel transcribed sequences neighbouring a translocation breakpoint associated with schizophrenia. Am. J. Med. Genet. 74: 82–90.PubMedGoogle Scholar
  60. Di Cristofano, A., M. Strazullo, L. Longo & G. La Mantia, 1995. Characterization and genomic mapping of the ZNF80 locus: expression of this zinc-finger gene is driven by a solitary LTR of ERV9 endogenous retroviral family. Nucleic Acids Res. 23: 2823–2830.PubMedGoogle Scholar
  61. Dierick, H.A., J.F. Mercer & T.W. Glover, 1997. A phosphoglycerate mutase brain isoform (PGAM 1) pseudogene is localized within the human Menkes disease gene (ATP7 A). Gene 198: 37–41.PubMedGoogle Scholar
  62. DiMarco, S.P., T.W. Glover, D.E. Miller, D. Reines & S.T. Warren, 1996. Transcription elongation factor SII (TCEA) maps to human chromosome 3p22 — > p21.3. Genomics 36: 185–188.PubMedGoogle Scholar
  63. Donnelly, S.R., T.E. Hawkins & S.E. Moss, 1999. A conserved nuclear element with a role in mammalian gene regulation. Hum. Mol. Genet. 8: 1723–1728.PubMedGoogle Scholar
  64. Dono, R., N. Montuori, M. Rocchi, L. De Ponti-Zilli, A. Ciccodicola & M.G. Persico, 1991. Isolation and characterization of the CRIPTO autosomal gene and its X-linked related sequence. Am. J. Hum. Genet. 49: 555–565.PubMedGoogle Scholar
  65. Dudov, K.P. & R.P. Perry, 1984. The gene family encoding the mouse ribosomal protein L32 contains a uniquely expressed intron-containing gene and an unmutated processed gene. Cell 37: 457–468.PubMedGoogle Scholar
  66. Ehrmann, I.E., P.S. Ellis, S. Mazeyrat, S. Duthie, N. Brockdorff, M.G. Mattei, M.A. Gavin, N.A. Affara, G.M. Brown, E. Simpson, M.J. Mitchell & D.M. Scott, 1998. Characterization of genes encoding translation initiation factor elF-2gamma in mouse and human: sex chromosome localization, escape from X-inactivation and evolution. Hum. Mol. Genet. 7: 1725–1737.PubMedGoogle Scholar
  67. Emi, M., A. Horii, N. Tomita, T. Nishide, M. Ogawa, T. Mori & K. Matsubara, 1988. Overlapping two genes in human DNA: a salivary amylase gene overlaps with a gamma-actin pseudogene that carries an integrated human endogenous retroviral DNA. Gene 62: 229–235.PubMedGoogle Scholar
  68. Ernstsson, S., S. Pierrou, M. Hulander, A. Cederberg, M. Hellqvist, P. Carlsson & S. Enerback, 1996. Characterization of the human forkhead gene FREAC-4. Evidence for regulation by Wilms' tumor suppressor gene (WT-1) and p53. J. Biol. Chem. 271: 21094–21099.PubMedGoogle Scholar
  69. Erusalimsky, J.D., S.F. Brooks, T. Herget, C. Morris & E. Rozengurt, 1991. Molecular cloning and characterization of the acidic 80-kDa protein kinase C substrate from rat brain. Identification as a glycoprotein. J. Biol. Chem. 266: 7073–7080.PubMedGoogle Scholar
  70. Fantin, V.R., B.E. Lavan, Q. Wang, N.A. Jenkins, D.J. Gilbert, N.G. Copeland, S.R. Keller & G.E. Lienhard, 1999. Cloning, tissue expression, and chromosomal location of the mouse insulin receptor substrate 4 gene. Endocrinology 140: 1329–1337.PubMedGoogle Scholar
  71. Feuchter, A.E., J.D. Freeman & D.L. Mager, 1992. Strategy for detecting cellular transcripts promoted by human endogenous long terminal repeats: identification of a novel gene (CDC4L) with homology to yeast CDC4. Genomics 13: 1237–1246.PubMedGoogle Scholar
  72. Feuchter-Murthy, A.E., F.J.D. & M.D.L. 1993. Splicing of a human retrovirus to a novel phospolipase A2 related gene. Nucleic Acids Res. 21: 135–143.PubMedGoogle Scholar
  73. Fitzgerald, J., W.M. Hutchison, and H.H. Dahl. 1992. Isolation and characterisation of the mouse pyruvate dehydrogenase El alpha genes. Biochim. Biophys. Acta 1131: 83–90.PubMedGoogle Scholar
  74. Foglio, M.H. & G. Duester, 1996. Characterization of the functional gene encoding mouse class III alcohol dehydrogenase (glutathione-dependent formaldehyde dehydrogenase) and an unexpressed processed pseudogene with an intact open reading frame. Eur. J. Biochem. 237: 496–504.PubMedGoogle Scholar
  75. Fornasari, D., E. Bataglioli, A. Flora, S. Terzano & F. Clementi, 1997. Structural and functional characterization of the human alpha 3 nicotinic subunit gene promoter. Molecular Pharmacol. 51: 250–261.Google Scholar
  76. Foster, J.W. & J.A. Graves, 1994. An SRY-related sequence on the marsupial X chromosome: implications for the evolution of the mammalian testis-determining gene. Proc. Natl. Acad. Sci. USA 91: 1927–1931.PubMedGoogle Scholar
  77. Fourel, G., C. Transy, B.C. Tennant & M.A. Buendia, 1992. Expression of the woodchuck N-myc2 retroposon in brain and in liver tumors is driven by a cryptic N-myc promoter. Mol. Cell. Biol. 12: 5336–5344.PubMedGoogle Scholar
  78. Fourel, G., C. Trepo, L. Bougueleret, B. Henglein, A. Ponzetto, P. Tiollais & M.A. Buendia, 1990. Frequent activation of N-myc genes by hepadnavirus insertion in woodchuck liver tumours. Nature 347: 294–298.PubMedGoogle Scholar
  79. Frank, S. & B. Zoll, 1998. Mouse HNF-3/fork head homolog-1-like gene: structure, chromosomal location, and expression in adult and embryonic kidney. DNA Cell. Biol. 17: 679–688.PubMedCrossRefGoogle Scholar
  80. Fratini, A., B.C. Powell & G.E. Rogers, 1993. Sequence, expression, and evolutionary conservation of a gene encoding a glycine/tyrosine-rich keratin-associated protein of hair. J. Biol. Chem. 268: 4511–4518.PubMedGoogle Scholar
  81. Frenkel, M.J., B.C. Powell, K.A. Ward, M.J. Sleigh & G.E. Rogers, 1989. The keratin BIIIB gene family: isolation of cDNA clones and structure of a gene and a related pseudogene. Genomics 4: 182–191.PubMedGoogle Scholar
  82. Fujii, T., K. Tamura, N.G. Copeland, D.J. Gilbert, N.A. Jenkins, K. Yomogida, H. Tanaka, Y. Nishimune, H. Nojima & Y. Abiko, 1999. Sperizin is a murine RING zinc-finger protein specifically expressed in Haploid germ cells. Genomics 57: 94–101.PubMedGoogle Scholar
  83. Gafvels, M., M. Olin, B.P. Chowdhary, T. Raudsepp, U. Andersson, B. Persson, M. Jansson, I. Bjorkhem & G. Eggertsen, 1999. Structure and chromosomal assignment of the sterol 12alpha-hydroxylase gene (CYP8B1) in human and mouse: eukaryotic cytochrome P-450 gene devoid of introns. Genomics 56: 184–196.PubMedGoogle Scholar
  84. Galili, N., H.S. Baldwin, J. Lund, R. Reeves, W. Gong, Z. Wang, B.A. Roe, B.S. Emanuel, S. Nayak, C. Mickanin, M.I. Budarf & C.A. Buck, 1997. A region of mouse chromosome 16 is syntenic to the DiGeorge, velocardiofacial syndrome minimal critical region. Genome Res. 7: 399.PubMedGoogle Scholar
  85. Gao, M., W. Rychlik & R.E. Rhoads, 1998. Cloning and characterization of human eIF4E genes. J. Biol. Chem. 273: 4622–4628.PubMedGoogle Scholar
  86. Gedeon, A.K., A. Colley, R. Jamieson, E.M. Thompson, J. Rogers, D. Sillence, G.E. Tiller, J.C. Mulley & J. Gecz, 1999. Identification of the gene (SEDL) causing X-linked spondyloepiphyseal dysplasia tarda. Nat Genet. 22: 400–404.PubMedGoogle Scholar
  87. Gentles, A.J. & S. Karlin, 1999. Why are human G-protein-coupled receptors predominantly intronless? Trends Genet. 15: 47–49.PubMedGoogle Scholar
  88. Gerber, A.M., M.A. O'Connell & W. Keller, 1997. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. Rna 3: 453–463.PubMedGoogle Scholar
  89. Glaichenhaus, N. & F. Cuzin, 1987. A role for ID repetitive sequences in growth-and transformation-dependent regulation of gene expression in rat fibroblasts. Cell. 50: 1081–1089.PubMedGoogle Scholar
  90. Goldenthal, M.J., J. Marin-Garcia & R. Ananthakrishnan, 1998. Cloning and molecular analysis of the human citrate synthase gene. Genome 41: 733–738.PubMedGoogle Scholar
  91. Goodchild, N.L., D.A. Wilkinson & D.L. Mager, 1992. A human endogenous long terminal repeat provides a polyadenylation signal to novel, alternatively spliced transcript in normal placenta. Gene 121: 287–294.PubMedGoogle Scholar
  92. Grant, D.M. M. Blum, A. Demierre & U.A. Meyer, 1989. Nucleotide sequence of an intronless gene for a human arylamine N-acetyltransferase related to polymorphic drug acetylation. Nucleic Acids Res. 17: 3978.PubMedGoogle Scholar
  93. Gromoll, J., E. Pekel & E. Nieschlag, 1996. The structure and organization of the human follicle-stimulating hormone receptor (FSHR) gene. Genomics 35: 308–311.PubMedGoogle Scholar
  94. Guehenneux, F., L. Duret, M.B. Callanan, R. Bouhas, S. Hayette, C. Berthet, C. Samarut, R. Rimokh, A.M. Birot, Q. Wang, J.P. Magaud & J.P. Rouault, 1997. Cloning of the mouse BTG3 gene and definition of a new gene family (the BTG family) involved in the negative control of the cell cycle. Leukemia. 11: 370–375.PubMedGoogle Scholar
  95. Guo, N., T. Mogues, S. Weremowicz, C.C. Morton & K.N. Sastry, 1998. The human ortholog of rhesus mannose-binding protein-A gene is an expressed pseudogene that localizes to chromosome 10. Mamm. Genome 9: 246–249.PubMedGoogle Scholar
  96. Hakim, I., N. Amariglio, Z. Grossman, F. Simoni Brok, S. Ohno & G. Rechavi, 1994. The genome of the THE I human transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence. Proc. Natl. Acad. Sci. USA 91: 7967–7969.PubMedGoogle Scholar
  97. Hamann, K.J., R.M. Ten, D.A. Loegering, R.B. Jenkins, M.T. Heise, C.R. Schad, L.R. Pease, G.J. Gleich & R.L. Barker, 1990. Structure and chromosome localization of the human eosinophil-derived neurotoxin and eosinophil cationic protein genes: evidence for intronless coding sequences in the ribonuclease gene superfamily. Genomics 7: 535–546.PubMedGoogle Scholar
  98. Hambor, J.E., J. Mennone, M.E. Coon, J.H. Hanke & P. Kavathas, 1993. Identification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8a gene. Mol. Cell Biol. 13: 7056–7070.PubMedGoogle Scholar
  99. Hara, Y., A.C. Rovescalli, Y. Kim & M. Nirenberg, 1992. Structure and evolution of four POU domain genes expressed in mouse brain. Proc. Natl. Acad. Sci. USA 89: 3280–3284.PubMedGoogle Scholar
  100. Harendza, C.J. & L.F. Johnson, 1990. Polyadenylylation signal of the mouse thymidylate synthase gene was created by insertion of an L1 repetitive element downstream of the open reading frame. Proc. Natl. Acad. Sci. USA 87: 2531–2535.PubMedGoogle Scholar
  101. Hart, P.E., J.N. Glantz, J.D. Orth, G.M. Poynter & J.L. Salisbury, 1999. Testis-specific murine centrin, Cetn 1: genomic characterization and evidence for retroposition of a gene encoding a centrosome protein. Genomics 60: 111–120.PubMedGoogle Scholar
  102. Hartl, M., J.T. Hutchins & P.K. Vogt, 1991. The chicken junD gene and its product. Oncogene 6: 1623–1631.PubMedGoogle Scholar
  103. Hattori, K., P. Angel, M.M. Le Beau & M. Karin, 1988. Structure and chromosomal localization of the functional intronless human JUN protooncogene. Proc. Natl. Acad. Sci USA 85:9148–9152.PubMedGoogle Scholar
  104. Haydock, P.V. & B.A. Dale, 1986. The repetitive structure of the profilaggrin gene as demonstrated using epidermal profilaggrin cDNA. J. Biol. Chem. 261: 12520–12525.PubMedGoogle Scholar
  105. Hendriksen, P.J., J.W. Hoogerbrugge, W.M. Baarends, P. de Boer, J.T. Vreeburg, E.A. Vos, T van der Lende & J.A. Grootegoed, 1997. Testis-specific expression of a functional retroposon encoding glucose-6-phosphate dehydrogenase in the mouse. Genomics 41: 350–359.PubMedGoogle Scholar
  106. Hennemann, H., E. Dahl, J.B. White, H.J. Schwarz, P.A. Lalley, S. Chang, B.J. Nicholson & K. Willecke, 1992. Two gap junction genes, connexin 31.1 and 30.3, are closely linked on mouse chromosome 4 and preferentially expressed in skin. J. Biol. Chem. 267: 17225–17233.PubMedGoogle Scholar
  107. Hentschel, C.C. & M.L. Birnstiel, 1981. The organization and expression of histone gene families. Cell. 25: 301–313.PubMedGoogle Scholar
  108. Heron, L., A. Virsolvy, F. Apiou, A. Le Cam & D. Bataille, 1999. Isolation, characterization, and chromosomal localization of the human ENSA gene that encodes alpha-endosulfine, a regulator of beta-cell K(ATP) channels. Diabetes 48: 1873–1876.PubMedGoogle Scholar
  109. Hewitt, S.M., G.C. Fraizer & G.F. Saunders, 1995. Transcriptional silencer of the Wilms' tumor gene WT1 contains an Alu repeat. J. Biol. Chem. 270: 17908–17912.PubMedGoogle Scholar
  110. Hirsch, A.H., S.B. Glantz, Y. Li, Y. You & C.S. Rubin, 1992. Cloning and expression of an intron-less gene for AKAP 75, an anchor protein for the regulatory subunit of cAMP-dependent protein kinase II beta. J. Biol. Chem. 267: 2131–2134.PubMedGoogle Scholar
  111. Hohlbaum, A.M. U. Krawinkel & P. Hemmerich, 1998. Structure and expression of a non-polyadenylated ribosome bound transcript carrying the sequence of human ribosomal protein L7 mRNA in antisense orientation. Biol. Chem. 379: 1193–1200.PubMedGoogle Scholar
  112. Hong, Y., K. Ohishi, N. Inoue, Y. Endo, T. Fujita, J. Takeda & T. Kinoshita, 1997. Structures and chromosomal localizations of the glycosylphosphatidylinositol synthesis gene PIGC and its pseudogene PIGCP1. Genomics. 44: 347–349.PubMedGoogle Scholar
  113. Hsu, D.W., M.J. Lin, T.L. Lee, S.C. Wen, X. Chen & C.K. Shen, 1999. Two major forms of DNA (cytosine-5) methyltransferase in human somatic tissues. Proc. Natl. Acad. Sci. USA 96: 9751–9756.PubMedGoogle Scholar
  114. Hui, P., X. Guo & P.G. Bradford, 1995. Isolation and functional characterization of the human gene encoding the myeloid zinc finger protein MZF-1. Biochemistry 34: 16493–16502.PubMedGoogle Scholar
  115. Humphrey, G.W., E.W. Englander & B.H. Howard, 1996. Specific binding sites for a pol III transcriptional repressor and pol II transcription factor YY1 within the internucleosomal spacer region in primate Alu repetitive elements. Gene. Expr. 6: 151–168.PubMedGoogle Scholar
  116. Hunt, C. & R.I. Morimoto, 1985. Conserved features of eukaryotic hsp70 genes revealed by comparison with the nucleotide sequence of human hsp70. Proc. Natl. Acad. Sci. USA 82: 6455–6459.PubMedGoogle Scholar
  117. Jackers, P., N. Clausse, M. Fernandez, A. Berti, F. Princen, U. Wewer, M.E. Sobel & V. Castronovo, 1996. Seventeen copies of the human 37 kDa laminin receptor precursor/p40 ribosome-associated protein gene are processed pseudogenes arisen from retropositional events. Biochim. Biophys. Acta. 1305: 98–104.PubMedGoogle Scholar
  118. Jackman, R.W., D.L. Beeler, L. Fritze, G. Soff & R.D. Rosenberg, 1987. Human thrombomodulin gene is intron depleted: nucleic acid sequences of the cDNA and gene predict protein structure and suggest sites of regulatory control. Proc. Natl. Acad. Sci. USA 84: 6425–6429.PubMedGoogle Scholar
  119. Jankowski, J.M., J.C. States & G.H. Dixon, 1986. Evidence of sequences resembling avian retrovirus long terminal repeats flanking the trout protamine gene. J. Mol. Evol. 23: 1–10.PubMedGoogle Scholar
  120. Jong, M.T., T.A. Gray, Y. Ji, C.C. Glenn, S. Saitoh, D.J. Driscoll & R.D. Nicholls, 1999. A novel imprinted gene, encoding a RING zinc-finger protein, and overlapping antisense transcript in the Prader-Willi syndrome critical region. Hum. Mol. Genet. 8: 783–793.PubMedGoogle Scholar
  121. Jun, D.Y., H.S. Kang, J.H. Seu & Y.H. Kim, 1997. Isolation and characterization of a processed pseudogene for murine cyclin D3. Mol. Cells 7: 278–283.PubMedGoogle Scholar
  122. Kapitonov, V.V. & J. Jurka, 1999. The long terminal repeat of an endogenous retrovirus induces alterantive splicing and encodes an additional carboxy-terminal sequence in the human leptin receptor. J. Mol. Evol. 48: 248–251.PubMedGoogle Scholar
  123. Kas, K., D. Stickens & J. Merregaert, 1995. Characterization of a processed pseudogene of human FAU1 on chromosome 18. Gene 160: 273–276.PubMedGoogle Scholar
  124. Kawaichi, M., C. Oka, S. Shibayama, A.E. Koromilas, N. Matsunami, Y. Hamaguchi & T. Honjo, 1992. Genomic organization of mouse J kappa recombination signal binding protein (RBP-J kappa) gene. J. Biol. Chem. 267: 4016–4022.PubMedGoogle Scholar
  125. Kedes, L.H., 1979. Histone genes and histone messengers. Annu. Rev. Biochem. 48: 837–870.PubMedGoogle Scholar
  126. Kim, J.H., C.Y. Yu, A. Bailey, R. Hardison & C.K. Shen, 1989. Unique sequence organization and erythroid cell-specific nuclear factor-binding of mammalian theta 1 globin promoters. Nucleic Acids Res. 17: 5687–5700.PubMedGoogle Scholar
  127. Kinoshita, S., S. Akira & T. Kishimoto, 1992. A member of the C/EBP family, NF-IL6 beta, forms a heterodimer and transcrip-tionally synergizes with NF-IL6. Proc. Natl. Acad. Sci. USA 89: 1473–1476.PubMedGoogle Scholar
  128. Kitagawa, K., X. Wang, I. Hatada, T. Yamaoka, H. Nojima, J. Inazawa, T. Abe, K. Mitsuya, M. Oshimura, A. Murata, et al. 1995. Isolation and mapping of human homologues of an imprinted mouse gene U2af1-rs1. Genomics 30: 257–263.PubMedGoogle Scholar
  129. Kleene, K.C., E. Mulligan, D. Steiger, K. Donohue & M.A. Mastrangelo, 1998. The mouse gene encoding the testis-specific isoform of Poly(A) binding protein (Pabp2) is an expressed retroposon: intimations that gene expression in spermatogenic cells facilitates the creation of new genes. J. Mol. Evol. 47: 275–281.PubMedGoogle Scholar
  130. Krane, D.E. & R.C. Hardison, 1990. Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals. Mol. Biol. Evol. 7: 1–8.PubMedGoogle Scholar
  131. Kress, M., Y. Barra, J.G. Seidman, G. Khoury & G. Jay, 1984. Functional insertion of an Alu type 2 (B2 SINE) repetitive sequence in murine class I genes. Science 226: 974–977.PubMedGoogle Scholar
  132. Krücken, J., O. Stamm, H.P. Schmitt-Wrede, A Mincheva, P. Lichter & F. Wunderlich, 1999. Spleen-specific expression of the malaria-inducible intronless mouse gene imap38. J. Biol. Chem. 274: 24383–24391.PubMedGoogle Scholar
  133. Kuczek, E.S. & G.E. Rogers, 1987. Sheep wool (glycine + tyrosine)-rich keratin genes. A family of low sequence homology. Eur. J. Biochem. 166: 79–85.PubMedGoogle Scholar
  134. Kudo, S., M.G. Mattei & M. Fukuda, 1995. Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain. Eur. J. Biochem. 231: 72–82.PubMedGoogle Scholar
  135. Kuhn, F., C. Lassing, A. Range, M. Mueller, T. Hunziker, A. Ziemiecki & A.C. Andres, 1999. Pmg-1 and pmg-2 constitute a novel family of KAP genes differentially expressed during skin and mammary gland development. Mech. Dev. 86: 193–196.PubMedGoogle Scholar
  136. Kuhn, R., E.S. Monuki & G. Lemke, 1991. The gene encoding the transcription factor SCIP has features of an expressed retroposon. Mol. Cell Biol. 11: 4642–4650.PubMedGoogle Scholar
  137. Kuzumaki, T., T. Tanaka, K. Ishikawa & K. Ogata, 1987. Rat ribosomal protein L35a multigene family: molecular structure and characterization of three L35a-related pseudogenes. Biochim. Biophys. Acta. 909: 99–106.PubMedGoogle Scholar
  138. Lahn, B.T. & D.C. Page, 1999. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. Nat. Genet. 21: 429–433.PubMedGoogle Scholar
  139. Laimins, L., K.M. Holmgren & G. Khoury, 1986. Transcriptional 'silencer' element in rat repetitive sequences associated with the rat insulin 1 gene locus. Proc. Natl. Acad. Sci. USA 83: 3151–3155.PubMedGoogle Scholar
  140. Lambotte, S., M. Veyhl, M. Kohler, A.I. Morrison-Shetlar, R.K. Kinne, M. Schmid & H. Koepsell, 1996. The human gene of a protein that modifies Na(+)-D-glucose co-transport. DNA Cell. Biol. 15: 769–777.PubMedGoogle Scholar
  141. Lan, M.S. Q. Li, J. Lu, W.S. Modi & A.L. Notkins, 1994. Genomic organization, 5′-upstream sequence, and chromosomal localization of an insulinoma-associated intronless gene, IA-1. J. Biol. Chem. 269: 14170–14174.PubMedGoogle Scholar
  142. Land, S.J., R.F. Jones & C.M. King, 1996. Genetic analysis of two rat acetyltransferases. Carcinogenesis 17: 1121–1126.PubMedGoogle Scholar
  143. Landschulz, W.H., P.F. Johnson, E.Y. Adashi, B.J. Graves & S.L. McKnight, 1988. Isolation of a recombinant copy of the gene encoding C/EBP. Genes. Dev. 2: 786–800.PubMedGoogle Scholar
  144. Lanza, F., M. Morales, C. de La Salle, J.P. Cazenave, K.J. Clemetson, T. Shimomura & D.R. Phillips, 1993. Cloning and characterization of the gene encoding the human platelet glycoprotein V. A member of the leucine-rich glycoprotein family cleaved during thrombin-induced platelet activation. J. Biol. Chem. 268: 20801–20807.PubMedGoogle Scholar
  145. Lawn, R.M., J. Adelman, A.E. Franke, C.M. Houck, M. Gross, R. Najarian & D.V. Goeddel, 1981. Human fibroblast interferon gene lacks introns. Nucleic Acids Res. 9: 1045–1052.PubMedGoogle Scholar
  146. Le Gallic, L. & P. Fort, 1997. Structure of the human ARHG locus encoding the Rho/Rac-like RhoG GTPase. Genomics 42: 157–160.PubMedGoogle Scholar
  147. Lee, I.Y., D. Westaway, A.F. Smit, K. Wang, J. Seto, L. Chen, C. Acharya, M. Ankener, D. Baskin, C. Cooper, H. Yao, S.B. Prusiner & L.E. Hood, 1998. Complete genomic sequence and analysis of the prion protein gene region from three mammalian species. Genome Res. 8: 1022–1037.PubMedGoogle Scholar
  148. Lee, T.H., S.L. Yu, S.U. Kim, Y.M. Kim, I. Choi, S.W. Kang, S.G. Rhee & D.Y. Yu. 1999. Characterization of the murine gene encoding 1-Cys peroxiredoxin and identification of highly homologous genes. Gene 234: 337–344.PubMedGoogle Scholar
  149. Levavasseur, F., W. Mandemakers, P. Visser, L. Broos, F. Grosveld, D. Zivkovic & D. Meijer, 1998. Comparison of sequence and function of the Oct-6 genes in zebrafish, chicken and mouse. Mech. Dev. 74: 89–98.PubMedGoogle Scholar
  150. Levinson, B., J.R. Bermingham, Jr., A. Metzenberg, S. Kenwrick, V. Chapman & J. Gitschier, 1992. Sequence of the human factor VIII-associated gene is conserved in mouse. Genomics 13: 862–865.PubMedGoogle Scholar
  151. Li, Q., A.L. Notkins & M.S. Lan, 1997. Molecular characterization of the promoter region of a neuroendocrine tumor marker, IA-1. Biochem. Biophys. Res. Commun. 236: 776–781.PubMedGoogle Scholar
  152. Liguori, G., L. De Gregorio, M. Tucci, C.T. Lago, A. Barra, T.A. Dragani & M. Persico, 1997. Mapping of the mouse Tdgf1 gene and Tdgf pseudogenes. Mamm. Genome. 8: 502–505.PubMedGoogle Scholar
  153. Liguori, G., M. Tucci, N. Montuori, R. Dono, C.T. Lago, F. Pacifico, F. Armenante & M.G. Persico, 1996. Characterization of the mouse Tdgf1 gene and Tdgf pseudogenes. Mamm. Genome. 7: 344–348.PubMedGoogle Scholar
  154. Lim, E.H. & S. Brenner, 1999. Short-range linkage relationships, genomic organisation and sequence comparisons of a cluster of the HSP70 genes in Fugu rubrips. Cell. Mol. Life Sci. 55: 668–678.PubMedGoogle Scholar
  155. Linnenbach, A.J., B.A. Seng, S. Wu, S. Robbins, M. Scollon, J.J. Pyrc, T. Druck & K. Huebner, 1993. Retroposition in a family of carcinoma-associated antigen genes. Mol. Cell. Biol. 13: 1507–1515.PubMedGoogle Scholar
  156. Linnenbach, A.J., J. Wojcierowski, S.A. Wu, J.J. Pyrc, A.H. Ross, B. Dietzschold, D. Speicher & H. Koprowski, 1989. Sequence investigation of the major gastrointestinal tumor-associated antigen gene family, GA733. Proc. Natl. Acad. Sci. USA 86: 27–31.PubMedGoogle Scholar
  157. Liu, A.Y. & B.A. Abraham, 1991. Subtractive cloning of a hybrid human endogenous retrovirus and calbindin gene in the prostate cell line PC3. Cancer Res. 51: 4107–4110.PubMedGoogle Scholar
  158. Liu, A.Y. & R.C. Bradner, 1993. Elevated expression of the human mitochondrial hinge protein gene in cancer. Cancer Res. 53: 2460–2465.PubMedGoogle Scholar
  159. Lowndes, N.F., P. Bushel, L. Mendelsohn J. Wu, M.Y. Yen & M. Allan, 1990. A short, highly repetitive element in intron-1 of the human c-Ha-ras gene acts as a block to transcriptional readthrough by a viral promoter. Mol. Cell. Biol. 10: 4990–4995.PubMedGoogle Scholar
  160. Ludwig, T., U. Ruther, R. Metzger, N.G. Copeland, N.A. Jenkins, P. Lobel & B. Hoflack, 1992. Gene and pseudogene of the mouse cation-dependent mannose 6-phosphate recetor. Genomic organization, expression, and chromosomal localization. J. Biol. Chem. 267: 12211–12219.PubMedGoogle Scholar
  161. Lum, R. & M.L. Linial, 1997. Tail-to-head arrangement of a partial chicken glyceraldehyde-3-phosphate dehydrogenase processed pseudogene. J. Mol. Evol. 45: 564–570.PubMedGoogle Scholar
  162. Lum, R. & M.L. Linial, 1998. Retrotransposition of nonviral RNAs in an avian packaging cell line. J. Virol. 72: 4057–4064.PubMedGoogle Scholar
  163. Lund, E.G., T.A. Kerr, J. Sakai, W.P. Li & D.W. Russell, 1998. cDNA cloning of mouse and human cholesterol 25-hydroxylases, polytopic membrane proteins that synthesize a potent oxysterol regulator of lipid metabolism. J. Biol. Chem. 273: 34316–34327.PubMedGoogle Scholar
  164. Luo, M., J. Shang, Z. Yang, C.P. Simkevich, C.L. Jackson, T.C. King & A.G. Rosmarin, 1999. Characterization and localization to chromosome 7 of psihGABPalpha, a human processed pseudogene related to the ets transcription factor, hGABPalpha. Gene 234: 119–126.PubMedGoogle Scholar
  165. MacLeod, A.R. & K. Talbot, 1983. A processed gene defining a gene family encoding a human non-muscle tropomyosin. J. Mol. Biol. 167: 523–537.PubMedGoogle Scholar
  166. Mager, D.L., 1989. Polyadenylation function and sequence variability of the long terminal repeats of the human endogenous retrovirus-like family RTVL-H. Virology 173: 591–599.PubMedGoogle Scholar
  167. Maichele, A.J., N.J. Farwell & J.S. Chamberlain, 1993. A B2 repeat insertion generates alternate structures of the mouse muscle gamma-phosphorylase kinase gene. Genomics 16: 139–149.PubMedGoogle Scholar
  168. Makalowski, W., G.A. Mitchell & D. Labuda, 1994. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10: 188–193.PubMedGoogle Scholar
  169. Makeyev, A.V., A.N. Chkheidze & S.A. Liebhaber, 1999. A set of highly conserved RNA-binding proteins, alphaCP-1 and alphaCP-2, implicated in mRNA stabilization, are coexpressed from an intronless gene and its intron-containing paralog. J. Biol. Chem. 274: 24849–24857.PubMedGoogle Scholar
  170. Manrow, R.E., A. Leone, M.S. Krug, W.H. Eschenfeldt & S.L. Berger, 1992. The human prothymosin alpha gene family contains several processed pseudogenes lacking deleterious lesions. Genomics 13: 319–331.PubMedGoogle Scholar
  171. Marron-Terada, P.G., K.E. Bollinger & N.M. Dahms, 1998. Characterization of truncated and glycosylation-deficient forms of the cation-dependent mannose 6-phosphate receptor expressed in baculovirus-infected insect cells. Biochemistry 37: 17223–17229.PubMedGoogle Scholar
  172. Martell, K.J., K.P. Vatsis & W.W. Weber, 1991. Molecular genetic basis of rapid and slow acetylation in mice. Mol. Pharmacol. 40: 218–227.PubMedGoogle Scholar
  173. Martignetti, J.A. & J. Brosius, 1993a. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proc. Natl. Acad. Sci. USA 90: 11563–11567.PubMedGoogle Scholar
  174. Martignetti, J.A. & J. Brosius, 1993b. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent. Proc. Natl. Acad. Sci. USA 90: 9698–9702.PubMedGoogle Scholar
  175. Martin, W.J., 1999. Melanoma growth stimulatory activity (MGSA-GRO-alpha) chemokine genes incorporated into an African green monkey simian cytomegalovirus-derived stealth virus. Exp. Mol. Pathol. 66: 15–18.PubMedGoogle Scholar
  176. Matsumine, H., M.A. Herbst, S.H. Ou, J.D. Wilson & M.J. McPhaul, 1991. Aromatase mRNA in the extragonadal tissues of chickens with the henny-feathering trait is derived from a distinctive promoter structure that contains a segment of a retroviral long terminal repeat. Functional organization of the Sebright, Leghorn, and Campine aromatase genes. J. Biol. Chem. 266: 19900–19907.PubMedGoogle Scholar
  177. Mazany, K.D., T. Peng, C.E. Watson, I. Tabas & K.J. Williams, 1998. Human chondroitin 6-sulfotransferase: cloning, gene structure, and chromosomal localization. Biochim. Biophys. Acta. 1407: 92–97.PubMedGoogle Scholar
  178. McCarrey, J.R. & K. Thomas, 1987. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326: 501–505.PubMedGoogle Scholar
  179. McHaffie, G.S. & S.H. Ralston, 1995. Origin of a negative calcium response element in an ALU-repeat: implications for regulation of gene expression by extracellular calcium. Bone 17: 11–14.PubMedGoogle Scholar
  180. McKinnon, R.D., T.M. Shinnick & J.G. Sutcliffe, 1986. The neuronal identifier element is a cis-acting positive regulator of gene expression. Proc. Natl. Acad. Sci. USA 83: 3751–3755.PubMedGoogle Scholar
  181. Michel, D., G. Chatelain, C. Mauduit, M. Benahmed & G. Brun, 1997. Recent evolutionary acquisition of alternative pre-mRNA splicing and 3′ processing regulations induced by intronic B2 SINE insertion. Nucleic Acids Res. 25: 3228–3234.PubMedGoogle Scholar
  182. Mihovilovic, M., Y. Mai, M. Herbstreith, F. Rubboli, P. Tarroni, F. Clementi & A.D. Roses, 1993. Splicing of an anti-sense Alu sequence generates a coding sequence variant for the alpha-3 subunit of a neuronal acetylcholine receptor. Biochem. Biophys. Res. Commun. 197: 137–144.PubMedGoogle Scholar
  183. Milner, C.M. & R.D. Campbell, 1990. Structure and expression of the three MHC-linked HSP70 genes. Immunogenetics 32: 242–251.PubMedGoogle Scholar
  184. Mishra, L., P. Yu, T. Cai, S.P. Monga & B. Mishra, 1999. Genomic structure, chromosomal mapping, and muscle-specific expression of a PH domain-associated intronless gene, cded/lior. Mamm. Genome. 10: 62–67.PubMedGoogle Scholar
  185. Misrahi, M., N. Ghinea, M.T. Vu Hai, H. Loosfelt, G. Meduri, M. Atger, B. Gross, A. Jolivet & E. Milgrom, 1995. [Pituitary glycoprotein hormone receptors]. Ann. Endocrinol. (Paris) 56: 487–493.Google Scholar
  186. Mitsui, S., A. Ohuchi, T. Adachi-Yamada, M. Hotta, R. Tsuboi & H. Ogawa, 1998. Structure and hair follicle-specific expression of genes encoding the rat high sulfur protein B2 family. Gene 208: 123–129.PubMedGoogle Scholar
  187. Miura, N., K. Iida, H. Kakinuma, X.L. Yang & T. Sugiyama, 1997. Isolation of the mouse (MFH-1) and human (FKHL 14) mesenchyme fork head-1 genes reveals conservation of their gene and protein structures. Genomics 41: 489–492.PubMedGoogle Scholar
  188. Moir, R.D. & G.H. Dixon, 1988. Characterization of a protamine gene from the chum salmon (Oncorhynchus keta). J. Mol. Evol. 27: 8–16.PubMedGoogle Scholar
  189. Moynihan, T.P., H.C. Ardley, J.P. Leek, J. Thompson, N.S. Brindle, A.F. Markham & P.A. Robinson, 1996. Characterization of a human ubiquitin-conjugating enzyme gene UBEL2L3. Mamm Genome. 7: 520–525.PubMedGoogle Scholar
  190. Mues, G.I., T.Z. Munn & J.D. Raese, 1986. A human gene family with sequence homology to Drosophila melanogaster Hsp70 heat shock genes. J. Biol. Chem. 261: 874–877.PubMedGoogle Scholar
  191. Mullersman, J.E. & L.M. Pfeffer, 1995. An Alu cassette in the cytoplasmic domain of an interferon receptor subunit. J. Interferon Cytokine Res. 15: 815–817.PubMedGoogle Scholar
  192. Murnane, J.P. & J.F. Morales, 1995. Use of a mammalian interspersed repetitive (MIR) element in the coding and processing sequences of mammalian genes. Nucleic Acids Res. 23: 2837–2839.PubMedGoogle Scholar
  193. Nagata, S., N. Mantei & C. Weissmann, 1980. The structure of one of the eight or more distinct chromosomal genes for human interferon-alpha. Nature 287: 401–408.PubMedGoogle Scholar
  194. Nakada, Y., H. Taniura, T. Uetsuki, J. Inazawa & K. Yoshikawa, 1998. The human chromosomal gene for necdin, a neuronal growth suppressor, in the Prader-Willi syndrome deletion region. Gene 213: 65–72.PubMedGoogle Scholar
  195. Newman, B. & Y. Dai, 1996. Transcription of c-mas protooncogene in the pig involves both tissue-specific promoters and alternative polyadenylation sites. Mol. Reprod. Dev. 44: 275–288.PubMedGoogle Scholar
  196. Neznanov, N.S. & R.G. Oshima, 1993. cis regulation of the keratin 18 gene in transgenic mice. Mol. Cell. Biol. 13: 1815–1823.PubMedGoogle Scholar
  197. Nhim, R.P., J.S. Lindsey & M.F. Wilkinson, 1997. A processed homeobox gene expressed in a stage, tissue and region specific manner in epididymis. Gene 185: 271–276.PubMedGoogle Scholar
  198. Nicole, S., P.S. White, H. Topaloglu, P. Beigthon, M. Salih, F. Hentati & B. Fontaine, 1999. The human CDC42 gene: genomic organization evidence for the existence of a putative pseudogene and exclusion as a SJS1 candidate gene. Hum. Genet. 105: 98–103.PubMedGoogle Scholar
  199. Niforas, P., G.M. Sanderson, C.H. Bird & P. Bird, 1993. Characterization of the mouse thrombomodulin gene and functional analysis of the 5′ flanking region in F9 teratocarcinoma cells. Biochim. Biophys. Acta. 1173: 179–187.PubMedGoogle Scholar
  200. Ninomiya, Y., M. Gordon, M. van der Rest, T. Schmid, T. Linsenmayer & B.R. Olsen, 1986. The developmentally regulated type X collagen gene contains a long open reading frame without introns. J. Biol. Chem. 261: 5041–5050.PubMedGoogle Scholar
  201. Nishimura, K., M. Liisanantti, Y. Muta, K. Kashiwagi, A. Shirahata, M. Janne, K. Kankare, O.A. Janne & K. Igarashi, 1998. Structure and activity of mouse S-adenosylmethionine decarboxylase gene promoters and properties of the encoded proteins. Bichem. J. 332: 651–659.Google Scholar
  202. Nojima, H., K. Kishi & H. Sokabe, 1987. Multiple calmodulin mRNA species are derived from two distinct genes. Mol. Cell. Biol. 7: 1873–1880.PubMedGoogle Scholar
  203. Norris, J., D. Fan, C. Aleman, J.R. Marks, P.A. Futreal, R.W. Wiseman, J.D. Iglehart, P.L. Deininger & D.P. McDonnell, 1995. Identification of a new subclass of Alu DNA repeats which can function as estrogen receptor-dependent transcriptional enhancers. J. Biol. Chem. 270: 22777–22782.PubMedGoogle Scholar
  204. Noyce, L., J. Conaty & A.A. Piper, 1997. Identification of a novel tissue-specific processed HPRT gene and comparison with X-linked gene transcription in the Australian marsupial Macropus robustus. Gene 186: 87–95.PubMedGoogle Scholar
  205. Noyce, L. & A.A. Piper, 1994. Isolation of a potentially functional hprt processed pseudogene from the hill kangaroo macropus robustus. Gene 150: 361–365.PubMedGoogle Scholar
  206. O'Neill, R.J., F.E. Brennan, M.L. Delbridge, R.H. Crozier & J.A. Graves, 1998. De novo insertion of an intron into the mammalian sex determining gene, SRY. Proc. Natl. Acad. Sci. USA 95: 1653–1657.PubMedGoogle Scholar
  207. Oei, S.L., J. Griesenbeck, M. Schweiger, V. Babich, A. Kropotov & N. Tomilin. 1997. Interaction of the transcription factor YY1 with human poly(ADP-ribosyl) transferase. Biochem. Biophys. Res. Commun. 240: 108–111.PubMedGoogle Scholar
  208. Okino, S.T., L.C. Quattrochi, H.J. Barnes, S. Osanto, K.J. Griffin, E.F. Johnson & R.H. Tukey, 1985. Cloning and characterization of cDNAs encoding 2,3,7,8-tetrachlorodibenzo-p-dioxin-inducible rabbit mRNAs for cytochrome P-450 isozymes 4 and 6. Proc. Natl. Acad. Sci. USA 82: 5310–5314.PubMedGoogle Scholar
  209. Oliva, R. & G.H. Dixon, 1989. Chicken protamine genes are intron-less. The complete genomic sequence and organization of the two loci. J. Biol. Chem. 264: 12472–12481.PubMedGoogle Scholar
  210. Oliviero, S. & P. Monaci, 1988. RNA polymerase III promoter elements enhance transcription of RNA polymerase II genes. Nucleic Acids Res. 16: 1285–1293.PubMedGoogle Scholar
  211. Owczarek, C.M., M.J. Layton, L.G. Robb, N.A. Nicola & C.G. Begley, 1996. Molecular basis of the soluble and membrane-bound forms of the murine leukemia inhibitory factor receptor alpha-chain. Expression in normal, gestating, and leukemia inhibitory factor nullizygous mice. J. Biol. Chem. 271: 5495–5504.PubMedGoogle Scholar
  212. Ozer, J., R. Chalkley & L. Sealy, 1993. Isolation of the CCAAT transcription factor subunit EFIA cDNA and a potentially functional EFIA processed pseudogene from Bos taurus: insights into the evolution of the EFIA/dbpB/YB-1 gene family. Gene 124: 223–230.PubMedGoogle Scholar
  213. Palmer, D.B., J.H. McVey, R. Purohit, J. Picard & P.J. Dyson, 1998. Characterization of a recent retroposon inseretion on mouse chromosome 2 and localization of the cognate parental gene to chromosome 11. Mamm. Genome 9: 103–106.PubMedGoogle Scholar
  214. Pan, Y., W.K. Decker, A.H. Huq & W.J. Craigen, 1999. Retro-transposition of glycerol kinase-related genes from the X chromosome to autosomes: functional and evolutionary aspects. Genomics 59: 282–290.PubMedGoogle Scholar
  215. Park, H., K. Baek, C. Jeon, K. Agarwal & O. Yoo, 1994. Characterization of the gene encoding the human transcriptional elongation factor TFIIS. Gene 139: 263–267.PubMedGoogle Scholar
  216. Paulson, K.E., A.G. Matera, and N. Deka & C.W. Schmid, 1987. Transcription of a human transposon-like sequence is usually directed by other promoters. Nucleic Acids Res. 15: 5199–5215.PubMedGoogle Scholar
  217. Peacock, R.E., T.J. Keen & C.F. Inglehearn, 1997. Analysis of a human gene homologous to rat ventral prostate. 1 protein. Genomics 46: 443–449.PubMedGoogle Scholar
  218. Pearsall, R.S., H. Shibata, A. Brozowska, K. Yoshino, K. Okuda, P.J. deJong, C. Plass, V.M. Chapman, Y. Hayashizaki & W.A. Held, 1996. Absence of imprinting in U2AFBPL, a human homologue of the imprinted mouse gene U2afbp-rs. Biochem. Biophys. Res. Commun. 222: 171–177.PubMedGoogle Scholar
  219. Peng, H.L., S.D. Cheng, J.H. Lee & H.Y. Chang, 1999. Identification of a novel family of human Rab-like small GTP-binding proteins. Proc. Natl. Sci. Counc. Repub. China B. 23: 38–44.PubMedGoogle Scholar
  220. Perez Jurado, L.A., Y.K. Wang, R. Peoples, A. Coloma, J. Cruces & U. Francke, 1998. A duplicate gene in the breakpoint regions of the 7q11.23 Williams-Beuren syndrome deletion encodes the initiator binding protein TFII-I and BAP-135, a phosphorylation target of BTK. Hum. Mol. Genet. 7: 325–334.PubMedGoogle Scholar
  221. Pérez, M.J., C. Leroux, A.S. Bonastre & P. Martin, 1994. Occurrence of a LINE sequence in the 3′ UTR of the goat alpha s1-casein E-encoding allele associated with reduced protein synthesis level. Gene 147: 179–187.PubMedGoogle Scholar
  222. Persson, K., O. Heby & F.G. Berger, 1999. The functional intronless S-adenosylmethionine decarboxylase gene of the mouse (Amd-2) is linked to the ornithine decarboxylase gene (Odc) on chromosome 12 and is present in distantly related species of the genus Mus. Mamm. Genome. 10: 784–788.PubMedGoogle Scholar
  223. Persson, K., I. Holm & O. Heby, 1995. Cloning and sequencing of an intronless mouse S-adenosylmethionine decarboxylase gene coding for a functional enzyme strongly expressed in the liver. J. Biol. Chem. 270: 5642–5648.PubMedGoogle Scholar
  224. Phelan, S.A., K.A. Johnson, D.R. Beier & B. Paigen, 1998. Characterization of the murine gene encoding Aop2 (antioxidant protein 2) and identification of two highly related genes. Genomics 54: 132–139.PubMedGoogle Scholar
  225. Piedrafita, F.J., R.B. Molander, G. Vansant, E.A. Orlova, M. Pfahl & W.F. Reynolds, 1996. An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element. J. Biol. Chem. 271: 14412–14420.PubMedGoogle Scholar
  226. Pietzsch, A., C. Buchler & G. Schmitz, 1998. Genomic organization, promoter cloning, and chromosomal localization of the Dif-2 gene. Biochem. Biophys. Res. Commun. 245: 651–657.PubMedGoogle Scholar
  227. Poindexter, K., N. Nelson, R.F. DuBose, R.A. Black & D.P. Cerretti, 1999. The identification of seven metalloproteinase-disintegrin (ADAM) genes from genomic libraries. Gene 237: 61–70.PubMedGoogle Scholar
  228. Porcellati, F., Y. Hosaka, T. Hlaing, M. Togawa, D.D. Larkin, A. Karihaloo, M.J. Stevens, P.D. Killen & D.A. Greene, 1999. Alternate splicing in human Na+-MI cotransporter gene yields differentially regulated transport isoforms. Am. J. Physiol. 276: C1325-C1337.PubMedGoogle Scholar
  229. Powell, B.C., G.R. Cam, M.J. Fietz & G.E. Rogers, 1986. Clustered arrangement of keratin intermediate filament genes. Proc. Natl. Acad. Sci. USA 83: 5048–5052.PubMedGoogle Scholar
  230. Powell, B.C., M.J. Sleigh, K.A. Ward & G.E. Rogers, 1983. Mammalian keratin gene families: organisation of genes coding for the B2 high-sulphur proteins os sheep wool. Nucleic Acids Res. 11: 5327–5346.PubMedGoogle Scholar
  231. Prezant, T.R., P. Kadioglu & S. Melmed, 1999. An intronless homolog of human proto-oncogene hPTTG is expressed in pituitary tumors: evidence for hPTTG family. J. Clin. Endocrinol. Metab. 84: 1149–1152.PubMedGoogle Scholar
  232. Prinsen, C.F., D.O. Weghuis, A.G. Kessel & J.H. Veerkamp, 1997. Identification of a human heart FABP pseudogene located on chromosome 13. Gene 193: 245–251.PubMedGoogle Scholar
  233. Quignon, F., C.A. Renard, P. Tiollais, M.A. Buendia & C. Transy, 1996. A functional N-myc2 retroposon in ground squirrels: implications for hepadnavirus-associated carcinogenesis. Oncogene 12: 2011–2017.PubMedGoogle Scholar
  234. Ravanat, C., M. Morales, D.O. Azorsa, S. Moog, S. Schuhler, P. Grunert, D. Loew, A. Van Dorsselaer, J.P. Cazenave & F. Lanza, 1997. Gene cloning of rat and mouse platelet glycoprotein V: identification of megakaryocyte-specific promoters and demonstration of functional thrombin cleavage. Blood 89: 3253–3262.PubMedGoogle Scholar
  235. Rebiere, M.C., P.N. Marche & T.J. Kindt, 1987. A rabbit class I major histocompatibility complex gene with a T cell-specific expression pattern. J. Immunol. 139: 2066–2074.PubMedGoogle Scholar
  236. Redolfi, E., C. Montagna, S. Mumm, M. Affer, L. Susani, R. Reinbold, F. Hol, P. Vezzoni, M. Cimino & I. Zucchi, 1998. Identification of CXorfl, a novel intronless gene in Xq27.3, expressed in human hippocampus. DNA Cell Biol. 17: 1009–1016.PubMedCrossRefGoogle Scholar
  237. Reinhardt, J., M. Veyhl, K. Wagner, S. Gambaryan, C. Dekel, A. Akhoundova, T. Korn & H. Koepsell, 1999. Cloning and characterization of the transport modifier RS1 from rabbit which was previously assumed to be specific for Na+-D-glucose contrasport. Biochim. Biophys. Acta. 1417: 131–143.PubMedGoogle Scholar
  238. Reinton, N., T.B. Haugen, S. Orstavik, B.S. Skalhegg, V. Hansson, T. Jahnsen & K. Tasken, 1998. The gene encoding the C gamma catalytic subunit of cAMP-dependent protein kinase is a transcribed retroposon. Genomics 49: 290–297.PubMedGoogle Scholar
  239. Relaix, F., X. Weng, G. Marazzi, E. Yang, N. Jenkins, S.E. Spence & D. Sassoon, 1996. Pw1, a novel zinc finger gene implicated in the myogenic and neuronal lineages. Dev. Biol. 177: 383–396.PubMedGoogle Scholar
  240. Renaudie, F., L. Boulanger, B. Grandchamp & C. Beaumont, 1995. (Cloning, characterization and expression of mouse ferritin L subunit gene). C.R. Acad. Sci. III. 318: 431–437.PubMedGoogle Scholar
  241. Renaudie, F., A.K. Yachou, B. Grandchamp, R. Jones & C. Beaumont, 1992. A second ferritin L subunit is encoded by an intronless gene in the mouse. Mamm. Genome 2: 143–149.PubMedGoogle Scholar
  242. Retief, J.D., R.J. Winkfein & G.H. Dixon, 1993. Evolution of the monotremes. The sequences of the protamine P1 genes of platypus and echidna. Eur. J. Biochem. 218: 457–461.PubMedGoogle Scholar
  243. Rhyner, J.A., M. Koller, I. Durussel Gerber, J.A. Cox & E.E. Strehler, 1992. Characterization of the human calmodulin-like protein expressed in Escherichia coli. Biochemistry 31: 12826–12832.PubMedGoogle Scholar
  244. Roberts, R.M., L. Liu, Q. Guo, D. Leaman & J. Bixby, 1998. The evolution of the type I interferons. J. Interferon Cytokine Res. 18: 805–816.PubMedGoogle Scholar
  245. Robertson, N.G., R.J. Pomponio, G.L. Mutter & C.C. Morton, 1991. Testis-specific expression of the human MYCL2 gene. Nucleic Acids Res. 19: 3129–3137.PubMedGoogle Scholar
  246. Robins, D.M. & L.C. Samuelson, 1992. Retrotransposons and the evolution of mammalian gene expression. Genetica 86: 191–201.PubMedGoogle Scholar
  247. Rothkopf, G.S., H.C. Telakowski, R.L. Stotish & C.B. Pickett, 1986. Multiplicity of glutathione S-transferase genes in the rat and association with a type 2 Alu repetitive element. Biochemistry 25: 993–1002.PubMedGoogle Scholar
  248. Rubtsov lu, P. & A.B. Vartapetian, 1995. (New intronless members of human prothymosin alpha genes). Mol. Biol. (Mosk) 29: 1320–1325.Google Scholar
  249. Ryskov, A.P., P.L. Ivanov, D.A. Kramerov & G.P. Georgiev, 1984. Universal orientation and 3′-terminal localization of repeated sequences in the B2 family of mRNA. Mol. Biol. Mosk. 18: 92–103.PubMedGoogle Scholar
  250. Saegusa, Y., M. Sato, I. Galli, T. Nakagawa, N. Ono, S.M. Iguchi-Ariga & H. Ariga, 1993. Stimulation of SV40 DNA replication and transcription by Alu family sequence. Biochim. Biophys. Acta 1172: 274–282.PubMedGoogle Scholar
  251. Saffer, J.D. & S.J. Thurston, 1989. A negative regulatory element with properties similar to those of enhancers is contained within an Alu sequence. Mol. Cell Biol. 9: 355–364.PubMedGoogle Scholar
  252. Saksela, K. & D. Baltimore, 1993. Negative regulation of immunoglobulin kappa light-chain gene transcription by a short sequence homologous to the murine B1 repetitive element. Mol. Cell. Biol. 13: 3698–3705.PubMedGoogle Scholar
  253. Samuelson, L.C, R.S. Phillips & L.J. Swanberg, 1996. Amylase gene structures in primates: retroposon insertions and promoter evolution. Mol. Biol. Evol. 13: 767–779.PubMedGoogle Scholar
  254. Samuelson, L.C., K. Wiebauer, G. Howard, R.M. Schmid, D. Koeplin & M.H. Meisler, 1991. Isolation of the murine ribonuclease gene Rib-1: structure and tissue specific expression in pancreas and partoid gland. Nucleic Acids Res. 19: 6935–6941.PubMedGoogle Scholar
  255. Samuelson, L.C., K. Wiebauer, C.M. Snow & M.H. Meisler, 1990 Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution. Mol. Cell. Biol. 10: 2513–2520.PubMedGoogle Scholar
  256. Sargent, C.A., I.J. Chalmers, M. Leversha & N.A. Affara, 1994a. A rearrangement on chromosome 5 of an expressed human betaglucuronidase pseudogene. Mamm. Genome 5: 791–796.PubMedGoogle Scholar
  257. Sargent, C.A., C. Young, S. Marsh, S.M. Ferguson & N.A. Affara, 1994b. The glycerol kinase gene family: structure of the Xp gene, and related intronless retroposons. Hum. Mol. Genet. 3: 1317–1324.PubMedGoogle Scholar
  258. Sasso, M.P., A. Carsana, E. Confalone, C. Cosi, S. Sorrentino, M. Viola, M. Palmieri, E. Russo & A. Furia, 1991. Molecular cloning of the gene encoding the bovine brain ribonuclease and its expression in different regions of the brain. Nucleic Acids Res. 19: 6469–6474.PubMedGoogle Scholar
  259. Schlüter, G. & W. Engel, 1995. The rat Prm3 gene is an intronless member of the protamine gene cluster and is expressed in haploid male germ cells. Cytogenet. Cell Genet. 71: 352–355.PubMedGoogle Scholar
  260. Schulte, A.M., S. Lai, A. Kurtz, F. Czubayko, A.T. Riegel & A. Wellstein, 1996. Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus. Proc. Natl. Acad. Sci. USA 93: 14759–14764.PubMedGoogle Scholar
  261. Schulte, A.M. & A. Wellstein, 1998. Structure and phylogenetic analysis of an endogenous retrovirus inserted into the human growth factor gene pleiotrophin. J Virol. 72: 6065–6072.PubMedGoogle Scholar
  262. Schweiger, M., S.L. Oei, H. Herzog, C. Menardi, R. Schneider, B. Auer & M. Hirsch-Kauffmann, 1995. Regulation of the human poly(ADR-ribosyl) transferase promoter via alternative DNA racket structures. Biochimie 77: 480–485.PubMedGoogle Scholar
  263. Sedlacek, Z., M.E.S. Dhorne-Pollet, C. Otto, D. Bock, G. Schütz & A. Poustka, 1999. Human and mouse XAP-5 and XAP-5-like (X5L) Genes: identification of an ancient functional retroposon differentially expressed in testis. Genomics 61: 125–132.PubMedGoogle Scholar
  264. Selig, S., S. Bruno, J.M. Scharf, C.H. Wang, E. Vitale, T.C. Gilliam & L.M. Kunkel, 1995. Expressed cadherin pseudogenes are localized to the critical region of the spinal muscular atrophy gene. Proc. Natl Acad. Sci. USA 92: 3702–3706.PubMedGoogle Scholar
  265. Sell, C., C.D. Chang, J. Koniecki, H.M. Chen & R. Baserga, 1992. A cryptopromoter is activated in the proliferating cell nuclear antigen gene of growth arrested cells. J. Cell. Physiol. 152: 177–184.PubMedGoogle Scholar
  266. Shashidharan, P., T.M. Michaelidis, N.K. Robakis, A. Kresovali, J. Papamatheakis & A. Plaitakis, 1994. Novel human glutamate dehydrogenase expressed in neural and testicular tissues encoded by an X-linked intronless gene. J. Biol. Chem. 269: 16971–16976.PubMedGoogle Scholar
  267. Shelley, C.S., E. Remold-O'Donnell, F.S. Rosen & A.S. Whitehead, 1990. Structure of the human sialophorin (CD43) gene. Identification of features atypical of genes encoding integral membrane proteins. Biochem. J. 270: 569–576.PubMedGoogle Scholar
  268. Shimamura, M., M. Nikaido, K. Ohshima & N. Okada, 1998. A SINE that acquired a role in signal transduction during evolution. Mol. Biol. Evol. 15: 923–925.PubMedGoogle Scholar
  269. Soares, M.B., E. Schon, A. Henderson, S.K. Karathanasis, R. Cate, S. Zeitlin, J. Chirgwin & A. Efstratiadis, 1985. RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. Mol. Cell. Biol. 5: 2090–2103.PubMedGoogle Scholar
  270. Soret, J., R. Gattoni, C. Guyon, A. Sureau, M. Popielarz, E. Le Rouzic, S. Dumon, F. Apiou, B. Dutrillaux, H. Voss, W. Ansorge, J. Stevenin & B. Perbal, 1998. Characterization of SRp46, a novel human SR splicing factor encoded by a PR264/SC35 retropseudogene. Mol. Cell Biol. 18: 4924–4934.PubMedGoogle Scholar
  271. Srikantha, T., D. Landsman & M. Bustin, 1987. Retropseudogenes for human chromosomal protein HMG-17. J. Mol. Biol. 197: 405–413.PubMedGoogle Scholar
  272. States, J.C., W. Connor, M.A. Wosnick, J.M. Aiken, L. Gedamu & G.H. Dixon, 1982. Nucleotide sequence of a protamine component CII gene of Salmo gairdnerii. Nucleic Acids Res. 10: 4551–4563.PubMedGoogle Scholar
  273. Stavenhagen, J.B. & D.M. Robins, 1988. An ancient provirus has imposed androgen regulation on the adjacent mouse sex-limited protein gene. Cell 55: 247–254.PubMedGoogle Scholar
  274. Strong, M., K.G. Chandy & G.A. Gutman, 1993. Molecular evolution of voltage-sensitive ion channel genes: on the origins of electrical excitability. Mol. Biol. Evol. 10: 221–242.PubMedGoogle Scholar
  275. Stros, M. & G.H. Dixon, 1993. A retropseudogene for non-histone chromosomal protein HMG-1. Biochim. Biophys. Acta. 1172: 231–235.PubMedGoogle Scholar
  276. Stros, M., J.D. Retief & G.H. Dixon, 1995. cDNA sequence and structure of a trout HMG-2 gene. Evidence for a trout-specific 3′-untranslated region. Gene 158: 181–187.PubMedGoogle Scholar
  277. Stutz, F. & G. Spohr, 1987. A processed gene coding for a sarcomeric actin in Xenopus laevis and Xenopus tropicalis. Embo J. 6: 1989–1995.PubMedGoogle Scholar
  278. Sugiyama, A., A. Kume, K. Nemoto, S.Y. Lee, Y. Asami, F. Nemoto, S. Nishimura & Y. Kuchino, 1989. Isolation and characterization of s-myc, a member of the rat myc gene family. Proc Natl. Acad. Sci. USA 86: 9144–9148.PubMedGoogle Scholar
  279. Sugiyama, A., K. Noguchi, C. Kitanaka, N. Katou, F. Tashiro, T. Ono, M.C. Yoshida & Y. Kuchino, 1999. Molecular cloning and chromosomal mapping of mouse intronless myc gene acting as a potent apoptosis inducer. Gene 226: 273–283.PubMedGoogle Scholar
  280. Sullivan, K.F. & C.A. Glass, 1991. CENP-B is a highly conserved mammalian centromere protein with homology to the helix-loop-helix family of proteins. Chromosoma 100: 360–370.PubMedGoogle Scholar
  281. Svineng, G., R. Fassler & S. Johansson, 1998. Identification of beta1C-2, a novel variant of the integrin beta1 subunit generated by utilization of an alternative splice acceptor site in exon C. Biochem. J. 330: 1255–1263.PubMedGoogle Scholar
  282. Takahashi, I., T. Nobukuni, H. Ohmori, M. Kobayashi, S. Tanaka, K. Ohshima, N. Okada, T. Masui, K. Hashimoto & S. Iwashita, 1998. Existence of bovine LINE repetitive insert that appears in the cDNA of bovine protein BCNT in ruminant, but not in human, genomes. Gene 211: 387–394.PubMedGoogle Scholar
  283. Takayama, Y., C. Wada, H. Kawauchi & M. Ono, 1989. Structures of two genes coding for melanin-concentrating hormone of chum salmon. Gene 80: 65–73.PubMedGoogle Scholar
  284. Takematsu, H., Y. Kozutsumi, A. Suzuki & T. Kawasaki, 1992. Molecular cloning of rabbit cytochrome b5 genes: evidence for the occurrence of two separate genes encoding the soluble and microsomal forms. Biochem. Biophys. Res. Commun. 185: 845–851.PubMedGoogle Scholar
  285. Takemura, H., M. Kaku, S. Kohno, H. Tanaka, R. Yoshida, K. Ishida, R. Mizukane, H. Koga, K. Hara, T. Usui & T. Ezaki, 1996. Cloning and expression of human defensin HNP-1 genomic DNA in Escherichia coli. J. Microbiol. Methods 25: 287–293.Google Scholar
  286. Theil, T., U. Zechner, C. Klett, S. Adolph & T. Moroy, 1994. Chromosomal localization and sequences of the murine Brn-3 family of developmental control genes. Cytogenet. Cell Genet. 66: 267–271.PubMedGoogle Scholar
  287. Thorey, I.S., G. Ceceña, W. Reynolds & R.G. Oshima, 1993. Alu sequence involvement in transcriptional insulation of the keratin 18 gene in transgenic mice. Mol. Cell. Biol. 13: 6742–6751.PubMedGoogle Scholar
  288. Tiffany, H.L., J.S. Handen & H.F. Rosenberg, 1996. Enhanced expression of the eosinophil-derived neurotoxin ribonuclease (RNS2) gene requires interaction between the promoter and intron. J. Biol. Chem. 271: 12387–12393.PubMedGoogle Scholar
  289. Ting, C.N., M.P. Rosenberg, C.M. Snow, L.C. Samuelson & M.H. Meisler, 1992. Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene. Genes Dev. 6: 1457–1465.PubMedGoogle Scholar
  290. Tnani, M. & B.A. Bayard, 1998. Lack of 2′,5′-oligoadenylate-dependent RNase expression in the human hepatoma cell line HepG2. Biochim. Biophys. Acta. 1402: 139–150.PubMedGoogle Scholar
  291. Tomilin, N.V., A.S. Iguchi & H. Ariga, 1990. Transcription and replication silencer element is present within conserved region of human Alu repeats interacting with nuclear protein. Febs Lett. 263: 69–72.PubMedGoogle Scholar
  292. Tosi, M., C. Duponchel, T. Meo & E. Couture-Tosi, 1989. Complement genes C1r and C1s feature an intronless serine protease domain closely related to haptoglobin. J. Mol. Biol. 208: 709–714.PubMedGoogle Scholar
  293. Tsytsykova, A.V., E.N. Tsitsikov, D.A. Wright, B. Futcher & R.S. Geha, 1998. The mouse genome contains two expressed intronless retroposed pseudogenes for the sentrin/sumo-1/PIC1 conjugating enzyme Ubc9. Mol. Immunol. 35: 1057–1067.PubMedGoogle Scholar
  294. Tucker, P.K. & B.L. Lundrigan, 1995. The nature of gene evolution of the mammalian Y chromosome: lessons from Sry. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 350: 221–227.PubMedGoogle Scholar
  295. Uetsuki, T., K. Takagi, H. Sugiura & K. Yoshikawa, 1996. Structure and expression of the mouse necdin gene. Identification of a postmitotic neuron-restrictive core promoter. J. Biol. Chem. 271: 918–924.PubMedGoogle Scholar
  296. Vansant, G. & W.F. Reynolds, 1995. The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc. Natl. Acad. Sci. USA 92: 8229–8233.PubMedGoogle Scholar
  297. Varghese, S. & H.M. Kronenberg, 1991. Rat thymosin beta 4 gene. Intron-containing gene and multiple retroposons. J. Biol. Chem. 266: 14256–14261.PubMedGoogle Scholar
  298. Vidal, F., E. Mougneau, N. Glaichenhaus, P. Vaigot, M. Darmon & F. Cuzin, 1993. Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences. Proc. Natl. Acad. Sci. USA 90: 208–212.PubMedGoogle Scholar
  299. Vogel, T., O. Dittrich, Y. Mehraein, F. Dechend, F. Schnieders & J. Schmidtke, 1998. Murine and human TSPYL genes: novel members of the TSPY-SET-NAP1L1 family. Cytogenet. Cell Genet. 81: 265–270.PubMedGoogle Scholar
  300. Wang, P.W., J.D. Eisenbart, S.P. Cordes, G.S. Barsh, M. Stoffel & M.M. Le Beau, 1999. Human KRML (MAFB): cDNA cloning genomic structure, and evaluation as a candidate tumor suppressor gene in myeloid leukemias. Genomics 59: 275–281.PubMedGoogle Scholar
  301. Watkins, S.P., M.K. Jeacock, D. Savva & D.A. Shepherd, 1991. Ovine trophoblast protein-one: evidence for possible glycosylation. Int. J. Biochem. 23: 1013–1018.PubMedGoogle Scholar
  302. Watson, C.E. & P.L. Davies, 1999. Recent and rapid amplification of the sperm basic nuclear protein genes in winter flounder. Biochim. Biophys. Acta. 1444: 337–345.PubMedGoogle Scholar
  303. Watson, R., M. Oskarsson & G.F. Vande Woude, 1982. Human DNA sequence homologous to the transforming gene (mos) of Moloney murine sarcoma virus. Proc. Natl. Acad. Sci. USA 79: 4078–4082.PubMedGoogle Scholar
  304. Weil, D., M.A. Power, G.C. Webb & C.L. Li, 1997. Antisense transcription of a murine FGFR-3 psuedogene during fetal development. Gene 187: 115–122.PubMedGoogle Scholar
  305. Weller, P.A., R. Critcher, P.N. Goodfellow, J. German & N.A. Ellis, 1995. The human Y chromosome homologue of XG: transcription of a naturally truncated gene. Hum. Mol. Genet. 4: 859–868.PubMedGoogle Scholar
  306. Wenger, R.H., M. Ayane, R. Bose, G. Kohler & P.J. Nielsen, 1991. The genes for a mouse hematopoietic differentiation marker called the heat-stable antigen. Eur. J. Immunol. 21: 1039–1046.PubMedGoogle Scholar
  307. Wenger, R.H., N. Kieffer, A.N. Wicki & K.J. Clemetson, 1988. Structure of the human blood platelet membrane glycoprotein Ib alpha gene. Biochem. Biophys. Res. Commun. 156: 389–395.PubMedGoogle Scholar
  308. Whitbread, L.A., K. Gregg & G.E. Rogers, 1991. The structure and expression of a gene encoding chick claw keratin. Gene 101: 223–229.PubMedGoogle Scholar
  309. Whitmore, S.A., C. Settasatian, J. Crawford, K.M. Lower, B. McCallum, R. Seshadri, C.J. Cornelisse, E.W. Moerland, A.M. Cleton-Jansen, A.J. Tipping, C.G. Mathew, M. Savnio, A. Savoia, P. Verlander, A.D. Auerbach, C. Van Berkel, J.C. Pronk, N.A. Doggett & D.F. Callen, 1998. Characterization and screening for mutations of the growth arrest-specific 11 (GAS11) and C16orf3 genes at 16q24.3 in breast cancer. Genomics 52: 325–331.PubMedGoogle Scholar
  310. Wiese, S., D.B. Murphy, A. Schlung, P. Burfeind, D. Schmundt, V. Schnulle, M.G. Mattei & U. Thies, 1995. The genes for human brain factor 1 and 2, members of the fork head gene family, are clustered on chromosome 14q. Biochim. Biophys. Acta. 1262: 105–112.PubMedGoogle Scholar
  311. Wilkie, T.M., D.J. Gilbert, A.S. Olsen, X.N. Chen, T.T. Amatruda, J.R. Korenberg, B.J. Trask, P. de Jong, R.R. Reed, M.I. Simon et al. 1992. Evolution of the mammalian G protein alpha subunit multigene family. Nat. Genet. 1: 85–91.PubMedGoogle Scholar
  312. Williams, M., M.S. Lyu, Y.L. Yang, E.P. Lin, R. Dunbrack, B. Birren, J. Cunningham & K. Hunter, 1999. ler5, a novel member of the slow-kinetics immediate-early genes. Genomics 55: 327–334.PubMedGoogle Scholar
  313. Williams, S.C., C.A. Cantwell & P.F. Johnson, 1991. A family of C/EBP-related proteins capable of forming covalently linked leucine zipper dimers in vitro. Genes Dev. 5: 1553–1567.PubMedGoogle Scholar
  314. Wirkner, U. & W. Pyerin, 1999. CK2alpha loci in the human genome: structure and transcriptional activity. Mol. Cell Biochem. 191: 59–64.PubMedGoogle Scholar
  315. Wu, J., G.J. Grindlay, P. Bushel, L. Mendelsohn & M. Allan, 1990. Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element. Mol. Cell Biol. 10: 1209–1216.PubMedGoogle Scholar
  316. Xu, G., P. O'Connell, J. Stevens & R. White, 1992. Characterization of human adenylate kinase 3 (AK3) cDNA and mapping of the AK3 pseudogene to an intron of the NF1 gene. Genomics 13: 537–542.PubMedGoogle Scholar
  317. Yagi, M., S. Edelhoff, C.M. Disteche & G.J. Roth, 1995. Human platelet glycoproteins V and IX: mapping of two leucine-rich glycoprotein genes to chromosome 3 and analysis of structures. Biochemistry 34: 16132–16137.PubMedGoogle Scholar
  318. Yang, G.C., N. Kunze, B. Baumgartner, Z.Y. Jiang, M. Sapp, R. Knippers & A. Richter, 1990. Molecular structures of two human DNA topoisomerase I retrosequences. Gene 91:247–253.PubMedGoogle Scholar
  319. Yang, Z., D. Boffelli, N. Boonmark, K. Schwartz & R. Lawn, 1998. Apolipoprotein(a) gene enhancer resides within a LINE element. J. Biol. Chem. 273: 891–897.PubMedGoogle Scholar
  320. Yasumasu, S., H. Shimada, K. Inohaya, K. Yamazaki, I. Iuchi, I. Yasumasu & K. Yamagami, 1996. Different exon-intron organizations of the genes for two astacin-like proteases, high choriolytic enzyme (choriolysin H) and low choriolytic enzyme (choriolysin L), the constituents of the fish hatching enzyme. Eur. J. Biochem. 237: 752–758.PubMedGoogle Scholar
  321. Yaswen, P., A. Smoll, J. Hosoda, G. Parry & M.R. Stampfer, 1992. Protein product of a human intronless calmodulin-like gene shows tissue-specific expression and reduced abundance in transformed cells. Cell Growth Differ. 3: 335–345.PubMedGoogle Scholar
  322. Yoshida, Y., S. Matsuda & T. Yamamoto, 1997. Cloning and characterization of the mouse tob gene. Gene 191: 109–113.PubMedGoogle Scholar
  323. Yoshimura, Y., H. Tanaka, M. Nozaki, K. Yomogida, K. Shimamura, T. Yasunaga & Y. Nishimune, 1999. Genomic analysis of male germ cell-specific actin capping protein alpha. Gene 237: 193–199.PubMedGoogle Scholar
  324. Youssouffian, H. & H. Lodish, 1993. Transcriptional inhibition of the murine erythroprotien receptor gene by an upstream repetitive elements. Mol. Cell Biol. 13: 98–104.Google Scholar
  325. Zaiß, D.M., & P.M. Kloetzel, 1999. A second gene encoding the mouse proteasome activator PA28beta subunit is part of a LINE1 element and is driven by a LINE1 promoter. J. Mol. Biol. 287: 829–835.PubMedGoogle Scholar
  326. Zakeri, Z.F., D.J. Wolgemuth & C.R. Hunt, 1988. Identification and sequence analysis of a new member of the mouse HSP 70 gene family and characterization of its unique cellular and developmental pattern of expression in the male germ line. Mol. Cell Biol. 8: 2925–2932.PubMedGoogle Scholar
  327. Zhend, H., D. Bhavsar, I. Dugast, E. Zappone & J. Drysdale, 1997. Conserved mutations in human ferritin H pseudogenes: a second functional sequence or an evolutionary quirk? Biochim. Biophys. Acta 1351: 150–156.Google Scholar
  328. Zheng, H.D., D. Bhavsar & J. Drysdale, 1995. An unusual human ferritin H sequence from chromosome 4. DNA Seq. 5: 173–175.PubMedGoogle Scholar
  329. Zheng, J.H., N.-S. Shunnosuke, M. Takahashi & M. Nonaka, 1992. Insertion of the B2 sequence into intron 13 is the only defect of the H-2 k C4 gene which causes low C4 production. Nucleic Acids Res. 20: 4975–4979.PubMedGoogle Scholar

References

  1. Baltimore, D., 1985. Retroviruses and retrotransposons: the role of reverse transcription in shaping the eukaryotic genome. Cell 40: 481–482.PubMedGoogle Scholar
  2. Becker, Y., 1996. A short introduction to the origin and molecular evolution of viruses. Virus Genes. 11: 73–77.Google Scholar
  3. Blackburn, E.H., 1992. Telomerases. Annu. Rev. Biochem. 61: 113–129.PubMedGoogle Scholar
  4. Britten, R.J., 1996. DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. Acad. Sci. USA 93: 9374–9377.PubMedGoogle Scholar
  5. Britten, R.J., 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177–182.PubMedGoogle Scholar
  6. 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.PubMedGoogle Scholar
  7. Brookfield, J.F., 1994. The human Alu SINE sequences — is there a role for selection in their evolution? Bioessays 16: 793–795.PubMedGoogle Scholar
  8. Brosius, J., 1991. Retroposons — seeds of evolution. Science 251: 753.PubMedGoogle Scholar
  9. Brosius, J., 1999a. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet. 15: 304–305.PubMedGoogle Scholar
  10. Brosius, J., 1999b. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115–134.PubMedGoogle Scholar
  11. Brosius, J., 1999c. Transmutation of tRNA over time. Nat. Genet. 22: 8–9.PubMedGoogle Scholar
  12. Brosius, J. & S.J. Gould., 1992. On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA'. Proc. Natl. Acad. Sci. USA 89: 10706–10710.PubMedGoogle Scholar
  13. Brosius, J. & S.J. Gould, 1993. Molecular constructivity. Nature 365: 102.PubMedGoogle Scholar
  14. Brosius, J., M.L. Palmer, P.J. Kennedy & H.F. Noller, 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75: 4801–4805.PubMedGoogle Scholar
  15. Brosius, J. & H. Tiedge, 1995. Neural BC1 RNA: Dendritic localization and transport, pp. 289–330, in Localized RNAs, edited by H.D. Lipshitz, R:G: Landes, Austin, TX.Google Scholar
  16. Brosius, J. & H. Tiedge, 1996. Reverse transcriptase — mediator of genomic plasticity. Virus Genes 11: 163–179.Google Scholar
  17. Cavalier-Smith, T., 1991. Intron phylogeny: a new hypothesis. Trends Genet. 7: 145–148.PubMedCrossRefGoogle Scholar
  18. Darnell, J.E., & W.F. Doolittle, 1986. Speculations on the early course of evolution. Proc. Natl. Acad. Sci. USA 83: 1271–1275.PubMedGoogle Scholar
  19. Deininger, P.L. & M.A. Batzer, 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183–193.PubMedGoogle Scholar
  20. 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.PubMedGoogle Scholar
  21. Deininger, P.L. & V.K. Slagel, 1988. Recently amplified Alu family members share a common parental Alu sequence. Mol. Cell. Biol. 8: 4566–4569.PubMedGoogle Scholar
  22. Deininger, P.L., H. Tiedge, J. Kim & J. Brosius. 1996. Evolution, expression, and possible function of a master gene for amplification of an interspersed repeated DNA family in rodents, edited by W.E. Cohn and K. Moldave. Progr. Nucleic. Acids Res. 52: 67–88.Google Scholar
  23. Diamond, J., 1997. Guns, Germs, and Steel: The Fates of Human Societies. W.W. Norton, New York.Google Scholar
  24. Doolittle, R.F. & D.F. Feng, 1992. Tracing the origin of retroviruses. Curr. Top. Microbiol. Immunol. 176: 195–211.PubMedGoogle Scholar
  25. Doolittle, W.F. & C. Sapienza, 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603.PubMedGoogle Scholar
  26. Doolittle, W.F., 1989. Hierarchical approaches to genome evolution. Can. J. Phil. 14Suppl.: 101–133.Google Scholar
  27. Dunham, I., N. Shimizu, B.A. Roe, S. Chissoe, A.R. Hunt, J.E. Collins, R. Bruskiewich, D.M. Beare, M. Clamp, L.J. Smink, R. Ainscough, J.P. Almeida, A. Babbage, C. Bagguley, J. Bailey, K. Barlow, K.N. Bates, O. Beasley, C.P. Bird, S. Blakey, A.M. Bridgeman, D. Buck, J. Burgess, W.D. Burrill & K.P. O'Brien, 1999. The DNA sequence of human chromosome 22. Nature 402: 489–495.PubMedGoogle Scholar
  28. Feng, Q., J.V. Moran, H.H. Kazazian, Jr. & J.D. Boeke, 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905–916.PubMedGoogle Scholar
  29. Flavell, A.J., 1995. Retroelements, reverse transcriptase and evolution. Comp. Biochem. Physiol. B. Biochem. Mol. Biol. 110: 3–15.PubMedGoogle Scholar
  30. Georgiev, G.P., 1984. Mobile genetic elements in animal cells and their biological significance. Eur. J. Biochem. 145: 203–220.PubMedGoogle Scholar
  31. Gilbert, W., 1978. Why genes in pieces? Nature 271: 501.PubMedGoogle Scholar
  32. Gould, S.J. & E.S. Vrba, 1982. Exaptation — a missing term in the science of form. Paleobiology 8: 4–15.Google Scholar
  33. Hickey, D.A., 1982. Selfish DNA: a sexually-transmitted nuclear parasite. Genetics 101: 519–531.PubMedGoogle Scholar
  34. Jacob, F., 1982. The Possible and the Actual. Pantheon Books, New York.Google Scholar
  35. Jordan, I.K., L.V. Matyunina & J.F. McDonald, 1999. Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc. Natl. Acad. Sci. USA 96: 12621–12625.PubMedGoogle Scholar
  36. Jurka, J., 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94: 1872–1877.PubMedGoogle Scholar
  37. Jurka, J., 1998. Repeats in genomic DNA mining and meaning. Curr. Opin. Struct. Biol. 8: 333–337.PubMedGoogle Scholar
  38. Jurka, J. & A. Milosavljevic, 1991. Reconstruction and analysis of human Alu genes. J. Mol. Evol. 32: 105–121.PubMedGoogle Scholar
  39. Kermekchiev, M., M. Pettersson, P. Matthias & W. Schaffner, 1991. Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling? Gene Expr. 1: 71–81.PubMedGoogle Scholar
  40. Kidwell, M.G. & D. Lisch, 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94: 7704–7711.PubMedGoogle Scholar
  41. Kim, J., J.A. Martignetti, M.R. Shen, J. Brosius & P. Deininger, 1994. Rodent BC1 RNA gene as a master gene for ID element amplification. Proc. Natl. Acad. Sci. USA 91: 3607–3611.PubMedGoogle Scholar
  42. Koch, A.L., 1972. Enzyme evolution: I. The importance of untranslatable intermediates. Genetics 72: 297–316.PubMedGoogle Scholar
  43. Kolosha, V.O. & S.L. Martin, 1995. Polymorphic sequences encoding the first open reading frame protein from LINE-1 ribonucleoprotein particles. J. Biol. Chem. 270: 2868–2873.PubMedGoogle Scholar
  44. Labuda, D. & G. Striker, 1989. Sequence conservation in Alu evolution. Nucleic Acids Res. 17: 2477–2491.PubMedGoogle Scholar
  45. Makalowski, W., G.A. Mitchell & D. Labuda, 1994. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10: 188–193.PubMedGoogle Scholar
  46. McClintock, B., 1948. Mutable loci in maize. Carnegie Inst. Wash. Yearbook 47: 155–169.Google Scholar
  47. McDonald, J.F., 1990. Macroevolution and retroviral elements. Bioscience 40: 183–191.Google Scholar
  48. McDonald, J.F., 1993. Evolution and consequences of transposable elements. Curr. Opin. Genet. Dev. 3: 855–864.PubMedGoogle Scholar
  49. McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10: 123–126.Google Scholar
  50. Nouvel, P., 1994. The mammalian genome shaping activity of reverse transcriptase. Genetica 93: 191–201.PubMedGoogle Scholar
  51. Ohshima, K., M. Hamada, Y. Terai & N. Okada, 1996. The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol. Cell. Biol. 16: 3756–3764.PubMedGoogle Scholar
  52. Okada, N., M. Hamada, I. Ogiwara & K. Ohshima, 1997. SINEs and LINEs share common 3′ sequences: a review. Gene 205: 229–243.PubMedGoogle Scholar
  53. Orgel, L.E. & Crick, F.H.C., 1980. Selfish DNA: the ultimate parasite. Nature 284: 604–607.PubMedGoogle Scholar
  54. Pardue, M.L., O.N. Danilevskaya, K. Lowenhaupt, F. Slot & K.L. Traverse, 1996. Drosophila telomeres: new views on chromosome evolution. Trends Genet. 12: 48–52.PubMedGoogle Scholar
  55. Pathak, V.K., and W.S. Hu, 1997. 'Might as well jump!' — Template switching by retroviral transcriptase, defective genome information, and recombination. Semin. Virol. 8: 141–150.Google Scholar
  56. Patience, C., D.A. Wilkinson & R.A. Weiss, 1997. Our retroviral heritage. Trends Genet. 13: 116–120.PubMedGoogle Scholar
  57. Poole, A., D. Jeffares & D. Penny, 1999. Early evolution: prokaryotes, the new kids on the block. Bioessays 21: 880–889.PubMedGoogle Scholar
  58. Quentin, Y., 1988. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J. Mol. Evol. 27: 194–202.PubMedGoogle Scholar
  59. Rose, M.R. & W.F. Doolittle, 1983. Molecular biological mechanisms of speciation. Science 220: 157–162.PubMedGoogle Scholar
  60. Schmid, C.W., 1998. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26: 4541–4550.PubMedGoogle Scholar
  61. Shapiro, J.A., 1992. Natural genetic engineering in evolution. Genetica 86: 99–111.PubMedGoogle Scholar
  62. Singer, M.F., 1995. Unusual reverse transcriptases. J. Biol. Chem. 270: 24623–24626.PubMedGoogle Scholar
  63. Tomilin, N.V., 1999. Control of genes by mammalian retroposons. Int. Rev. Cytol. 186: 1–48.PubMedCrossRefGoogle Scholar
  64. Walsh, C.P., J.R. Chaillet & T.H. Bestor, 1998. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20: 116–117.PubMedGoogle Scholar
  65. Wessler, S.R., T.E. Bureau & S.E. White, 1995. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814–821.PubMedGoogle Scholar
  66. Willard, C., H.T. Nguyen & C.W. Schmid, 1987. Existence of at least three distinct Alu subfamilies. J. Mol. Evol. 26: 180–186.PubMedGoogle Scholar
  67. Woese, C.R., R. Gutell, R. Gupta & H.F. Noller, 1983. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 47: 621–669.PubMedGoogle Scholar
  68. Wolffe, A.P. & M.A. Matzke, 1999. Epigenetics: regulation through repression. Science 286: 481–486.PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 1999

Authors and Affiliations

  • Jürgen Brosius
    • 1
  1. 1.Institute of Experimental Pathology/Molecular Neurobiology, ZMBEUniversity of MünsterMünsterGermany (Phone: +

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