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’.
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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Blum, M., M. Heim & U.A. Meyer, 1990b. Nucleotide sequence of rabbit NAT1 encoding monomorphic arylamine Nacetyltransferase. Nucleic Acids Res. 18: 5287.
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.
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.
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.
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.
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.
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.
Brosius, J., 1999. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet. 15: 304–305.
Brunovskis, P. & H.J. Kung, 1996. Retrotransposition and herpesvirus evolution. Virus Genes. 11: 259–270.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Clemens, M.J. 1987. A potential role for RNA transcribed from B2 repeats in the regulation of mRNA stability. Cell 49: 157–158.
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.
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.
Crowe, M.L., B.N. Perry & I.F. Connerton, 1996. Olfactory receptor-encoding genes and pseudogenes are expressed in humans. Gene 169: 247–249.
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.
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.
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.
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.
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.
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.
DeChiara, T.M. & J. Brosius, 1987. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc. Natl. Acad. Sci. USA 84: 2624–2628.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Gao, M., W. Rychlik & R.E. Rhoads, 1998. Cloning and characterization of human eIF4E genes. J. Biol. Chem. 273: 4622–4628.
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.
Gentles, A.J. & S. Karlin, 1999. Why are human G-protein-coupled receptors predominantly intronless? Trends Genet. 15: 47–49.
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.
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.
Goldenthal, M.J., J. Marin-Garcia & R. Ananthakrishnan, 1998. Cloning and molecular analysis of the human citrate synthase gene. Genome 41: 733–738.
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.
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.
Gromoll, J., E. Pekel & E. Nieschlag, 1996. The structure and organization of the human follicle-stimulating hormone receptor (FSHR) gene. Genomics 35: 308–311.
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.
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.
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.
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.
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.
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.
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.
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.
Hartl, M., J.T. Hutchins & P.K. Vogt, 1991. The chicken junD gene and its product. Oncogene 6: 1623–1631.
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.
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.
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.
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.
Hentschel, C.C. & M.L. Birnstiel, 1981. The organization and expression of histone gene families. Cell. 25: 301–313.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Kas, K., D. Stickens & J. Merregaert, 1995. Characterization of a processed pseudogene of human FAU1 on chromosome 18. Gene 160: 273–276.
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.
Kedes, L.H., 1979. Histone genes and histone messengers. Annu. Rev. Biochem. 48: 837–870.
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.
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.
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.
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.
Krane, D.E. & R.C. Hardison, 1990. Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals. Mol. Biol. Evol. 7: 1–8.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Land, S.J., R.F. Jones & C.M. King, 1996. Genetic analysis of two rat acetyltransferases. Carcinogenesis 17: 1121–1126.
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.
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.
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.
Le Gallic, L. & P. Fort, 1997. Structure of the human ARHG locus encoding the Rho/Rac-like RhoG GTPase. Genomics 42: 157–160.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Liu, A.Y. & R.C. Bradner, 1993. Elevated expression of the human mitochondrial hinge protein gene in cancer. Cancer Res. 53: 2460–2465.
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.
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.
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.
Lum, R. & M.L. Linial, 1998. Retrotransposition of nonviral RNAs in an avian packaging cell line. J. Virol. 72: 4057–4064.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
McCarrey, J.R. & K. Thomas, 1987. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326: 501–505.
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.
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.
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.
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.
Milner, C.M. & R.D. Campbell, 1990. Structure and expression of the three MHC-linked HSP70 genes. Immunogenetics 32: 242–251.
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.
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.
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.
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.
Moir, R.D. & G.H. Dixon, 1988. Characterization of a protamine gene from the chum salmon (Oncorhynchus keta). J. Mol. Evol. 27: 8–16.
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.
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.
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.
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.
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.
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.
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.
Neznanov, N.S. & R.G. Oshima, 1993. cis regulation of the keratin 18 gene in transgenic mice. Mol. Cell. Biol. 13: 1815–1823.
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.
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.
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.
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.
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.
Nojima, H., K. Kishi & H. Sokabe, 1987. Multiple calmodulin mRNA species are derived from two distinct genes. Mol. Cell. Biol. 7: 1873–1880.
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.
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.
Noyce, L. & A.A. Piper, 1994. Isolation of a potentially functional hprt processed pseudogene from the hill kangaroo macropus robustus. Gene 150: 361–365.
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.
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.
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.
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.
Oliviero, S. & P. Monaci, 1988. RNA polymerase III promoter elements enhance transcription of RNA polymerase II genes. Nucleic Acids Res. 16: 1285–1293.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Robins, D.M. & L.C. Samuelson, 1992. Retrotransposons and the evolution of mammalian gene expression. Genetica 86: 191–201.
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.
Rubtsov lu, P. & A.B. Vartapetian, 1995. (New intronless members of human prothymosin alpha genes). Mol. Biol. (Mosk) 29: 1320–1325.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Srikantha, T., D. Landsman & M. Bustin, 1987. Retropseudogenes for human chromosomal protein HMG-17. J. Mol. Biol. 197: 405–413.
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.
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.
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.
Stros, M. & G.H. Dixon, 1993. A retropseudogene for non-histone chromosomal protein HMG-1. Biochim. Biophys. Acta. 1172: 231–235.
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.
Stutz, F. & G. Spohr, 1987. A processed gene coding for a sarcomeric actin in Xenopus laevis and Xenopus tropicalis. Embo J. 6: 1989–1995.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Varghese, S. & H.M. Kronenberg, 1991. Rat thymosin beta 4 gene. Intron-containing gene and multiple retroposons. J. Biol. Chem. 266: 14256–14261.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Whitbread, L.A., K. Gregg & G.E. Rogers, 1991. The structure and expression of a gene encoding chick claw keratin. Gene 101: 223–229.
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.
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.
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.
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.
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.
Wirkner, U. & W. Pyerin, 1999. CK2alpha loci in the human genome: structure and transcriptional activity. Mol. Cell Biochem. 191: 59–64.
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.
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.
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.
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.
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.
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.
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.
Yoshida, Y., S. Matsuda & T. Yamamoto, 1997. Cloning and characterization of the mouse tob gene. Gene 191: 109–113.
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.
Youssouffian, H. & H. Lodish, 1993. Transcriptional inhibition of the murine erythroprotien receptor gene by an upstream repetitive elements. Mol. Cell Biol. 13: 98–104.
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.
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.
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.
Zheng, H.D., D. Bhavsar & J. Drysdale, 1995. An unusual human ferritin H sequence from chromosome 4. DNA Seq. 5: 173–175.
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.
References
Baltimore, D., 1985. Retroviruses and retrotransposons: the role of reverse transcription in shaping the eukaryotic genome. Cell 40: 481–482.
Becker, Y., 1996. A short introduction to the origin and molecular evolution of viruses. Virus Genes. 11: 73–77.
Blackburn, E.H., 1992. Telomerases. Annu. Rev. Biochem. 61: 113–129.
Britten, R.J., 1996. DNA sequence insertion and evolutionary variation in gene regulation. Proc. Natl. Acad. Sci. USA 93: 9374–9377.
Britten, R.J., 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177–182.
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.
Brookfield, J.F., 1994. The human Alu SINE sequences — is there a role for selection in their evolution? Bioessays 16: 793–795.
Brosius, J., 1991. Retroposons — seeds of evolution. Science 251: 753.
Brosius, J., 1999a. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet. 15: 304–305.
Brosius, J., 1999b. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115–134.
Brosius, J., 1999c. Transmutation of tRNA over time. Nat. Genet. 22: 8–9.
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.
Brosius, J. & S.J. Gould, 1993. Molecular constructivity. Nature 365: 102.
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.
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.
Brosius, J. & H. Tiedge, 1996. Reverse transcriptase — mediator of genomic plasticity. Virus Genes 11: 163–179.
Cavalier-Smith, T., 1991. Intron phylogeny: a new hypothesis. Trends Genet. 7: 145–148.
Darnell, J.E., & W.F. Doolittle, 1986. Speculations on the early course of evolution. Proc. Natl. Acad. Sci. USA 83: 1271–1275.
Deininger, P.L. & M.A. Batzer, 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183–193.
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.
Deininger, P.L. & V.K. Slagel, 1988. Recently amplified Alu family members share a common parental Alu sequence. Mol. Cell. Biol. 8: 4566–4569.
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.
Diamond, J., 1997. Guns, Germs, and Steel: The Fates of Human Societies. W.W. Norton, New York.
Doolittle, R.F. & D.F. Feng, 1992. Tracing the origin of retroviruses. Curr. Top. Microbiol. Immunol. 176: 195–211.
Doolittle, W.F. & C. Sapienza, 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603.
Doolittle, W.F., 1989. Hierarchical approaches to genome evolution. Can. J. Phil. 14Suppl.: 101–133.
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.
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.
Flavell, A.J., 1995. Retroelements, reverse transcriptase and evolution. Comp. Biochem. Physiol. B. Biochem. Mol. Biol. 110: 3–15.
Georgiev, G.P., 1984. Mobile genetic elements in animal cells and their biological significance. Eur. J. Biochem. 145: 203–220.
Gilbert, W., 1978. Why genes in pieces? Nature 271: 501.
Gould, S.J. & E.S. Vrba, 1982. Exaptation — a missing term in the science of form. Paleobiology 8: 4–15.
Hickey, D.A., 1982. Selfish DNA: a sexually-transmitted nuclear parasite. Genetics 101: 519–531.
Jacob, F., 1982. The Possible and the Actual. Pantheon Books, New York.
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.
Jurka, J., 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94: 1872–1877.
Jurka, J., 1998. Repeats in genomic DNA mining and meaning. Curr. Opin. Struct. Biol. 8: 333–337.
Jurka, J. & A. Milosavljevic, 1991. Reconstruction and analysis of human Alu genes. J. Mol. Evol. 32: 105–121.
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.
Kidwell, M.G. & D. Lisch, 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94: 7704–7711.
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.
Koch, A.L., 1972. Enzyme evolution: I. The importance of untranslatable intermediates. Genetics 72: 297–316.
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.
Labuda, D. & G. Striker, 1989. Sequence conservation in Alu evolution. Nucleic Acids Res. 17: 2477–2491.
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.
McClintock, B., 1948. Mutable loci in maize. Carnegie Inst. Wash. Yearbook 47: 155–169.
McDonald, J.F., 1990. Macroevolution and retroviral elements. Bioscience 40: 183–191.
McDonald, J.F., 1993. Evolution and consequences of transposable elements. Curr. Opin. Genet. Dev. 3: 855–864.
McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10: 123–126.
Nouvel, P., 1994. The mammalian genome shaping activity of reverse transcriptase. Genetica 93: 191–201.
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.
Okada, N., M. Hamada, I. Ogiwara & K. Ohshima, 1997. SINEs and LINEs share common 3′ sequences: a review. Gene 205: 229–243.
Orgel, L.E. & Crick, F.H.C., 1980. Selfish DNA: the ultimate parasite. Nature 284: 604–607.
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.
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.
Patience, C., D.A. Wilkinson & R.A. Weiss, 1997. Our retroviral heritage. Trends Genet. 13: 116–120.
Poole, A., D. Jeffares & D. Penny, 1999. Early evolution: prokaryotes, the new kids on the block. Bioessays 21: 880–889.
Quentin, Y., 1988. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J. Mol. Evol. 27: 194–202.
Rose, M.R. & W.F. Doolittle, 1983. Molecular biological mechanisms of speciation. Science 220: 157–162.
Schmid, C.W., 1998. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26: 4541–4550.
Shapiro, J.A., 1992. Natural genetic engineering in evolution. Genetica 86: 99–111.
Singer, M.F., 1995. Unusual reverse transcriptases. J. Biol. Chem. 270: 24623–24626.
Tomilin, N.V., 1999. Control of genes by mammalian retroposons. Int. Rev. Cytol. 186: 1–48.
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.
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.
Willard, C., H.T. Nguyen & C.W. Schmid, 1987. Existence of at least three distinct Alu subfamilies. J. Mol. Evol. 26: 180–186.
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.
Wolffe, A.P. & M.A. Matzke, 1999. Epigenetics: regulation through repression. Science 286: 481–486.
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Brosius, J. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107, 209–238 (1999). https://doi.org/10.1023/A:1004018519722
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DOI: https://doi.org/10.1023/A:1004018519722