Genetica

, Volume 118, Issue 2–3, pp 99–115

The Contribution of RNAs and Retroposition to Evolutionary Novelties

  • Jürgen Brosius
Article

Abstract

Retroposition is an ancient process dating back to the conversion of RNA to DNA genomes. Nevertheless, it continues to make tremendous structural and functional contributions to extant genomes. This process and the endurance, or even renaissance, of an RNA world in many lineages sheds a new light on the Central Dogma of Molecular Biology. The question of why reverse transcriptase has survived billions of years without an apparent cellular function is discussed. Retroposition constitutes one of the pervasive conflicts, in this case between host genome on one hand and mobile genetic elements on the other, that fuel the evolutionary process. It is obvious that retroposition has, thus far, contributed numerous useful novelties to genomes.

genetic novelties genome evolution genome expansion and shrinkage retroposition survival of reverse transcriptase 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Amrein, H. & R. Axel, 1997. Genes expressed in neurons of adult male Drosophila. Cell 88: 459-469.PubMedGoogle Scholar
  2. Ariel, I., N. de Groot & A. Hochberg, 2000. Imprinted H19 gene expression in embryogenesis and human cancer: the oncofetal connection. Am. J. Med. Genet. 91: 46-50.PubMedGoogle Scholar
  3. Avner, P. & E. Heard, 2001. X-chromosome inactivation: counting, choice and initiation. Nat. Rev. Genet. 2: 59-67.PubMedGoogle Scholar
  4. Bachellerie, J.-P., J. Cavaillé & A. Hüttenhofer, 2002. The expanding snoRNA world. Biochimie 84: 775-790.PubMedGoogle Scholar
  5. Bailey, J.A., L. Carrel, A. Chakravarti & E.E. Eichler, 2000. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. P. Natl. Acad. Sci. USA 97: 6634-6639.Google Scholar
  6. Bailey, J.A., A.M. Yavor, L. Viggiano, D. Misceo, J.E. Horvath et al., 2002. Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am. J. Hum. Genet. 70: 83-100.PubMedGoogle Scholar
  7. Basile, V., A. Vicente, J.A. Martignetti, B.V. Skryabin, J. Brosius et al., 1998. Assignment of the human BC200 RNA gene (BCYRN1) to chromosome 2p16 by radiation hybrid mapping. Cytogenet. Cell. Genet. 82: 271-272.PubMedGoogle Scholar
  8. Batzer, M.A. & P.L. Deininger, 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3: 370-379.PubMedGoogle Scholar
  9. Benzow, K.A. & M.D. Koob, 2002. The KLHL1-antisense transcript (KLHL1AS) is evolutionarily conserved. Mamm. Genome 13: 134-141.PubMedGoogle Scholar
  10. Betran, E., W. Wang, L. Jin & M. Long, 2002. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol. 19: 654-663.PubMedGoogle Scholar
  11. Blackburn, E.H., 1991. Telomeres. Trends Biochem. Sci. 16: 378-381.PubMedGoogle Scholar
  12. Boumil, R.M. & J.T. Lee, 2001. Forty years of decoding the silence in X-chromosome inactivation. Hum. Mol. Genet. 10: 2225-2232.PubMedGoogle Scholar
  13. Brenner, S., 1998. Refuge of spandrels. Curr. Biol. 8: R669.PubMedGoogle Scholar
  14. Bridges, C., 1936. The Bar 'gene': a duplication. Science: 83: 210-211.Google Scholar
  15. Britten, R.J., 1996. DNA sequence insertion and evolutionary variation in gene regulation. P. Natl. Acad. Sci. USA 93: 9374-9377.Google Scholar
  16. Britten, R.J., 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177-182.PubMedGoogle Scholar
  17. Brosius, J., 1991. Retroposons-seeds of evolution. Science 251: 753.PubMedGoogle Scholar
  18. Brosius, J., 1999a. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107: 209-238.PubMedGoogle Scholar
  19. Brosius, J., 1999b. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet. 15: 304-305.PubMedGoogle Scholar
  20. Brosius, J., 1999c. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115-134.PubMedGoogle Scholar
  21. Brosius, J., 1999d. Transmutation of tRNA over time. Nat. Genet. 22: 8-9.PubMedGoogle Scholar
  22. Brosius, J., 2003a Echoes from the past-are we still in an RNP world? (submitted).Google Scholar
  23. Brosius, J., 2003b. Gene duplication and other evolutionary strategies: from the RNA world to the future. J. Struct. Funct. Genomics 3: 1-17.PubMedGoogle Scholar
  24. Brosius, J. & S.J. Gould, 1992. On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA'. P. Natl. Acad. Sci. USA 89: 10706-10710.Google Scholar
  25. Brosius, J. & S.J. Gould, 1993. Molecular constructivity. Nature 365: 102.Google Scholar
  26. Brosius, J. & H. Tiedge, 1995a. 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
  27. Brosius, J. & H. Tiedge, 1995b. Reverse transcriptase: mediator of genomic plasticity. Virus Genes 11: 163-179.PubMedGoogle Scholar
  28. Brosius, J. & H. Tiedge, 2001. Dendritic BC1 RNA: intracellular transport and activity-dependent modulation, pp. 129-138 in Cell Polarity and Subcellular RNA Localization, edited by D. Richter. Springer Verlag, Berlin.Google Scholar
  29. Bussemakers, M.J., A. van Bokhoven, G.W. Verhaegh, F.P. Smit, H.F. Karthaus et al., 1999. DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. Cancer Res. 59: 5975-5979.PubMedGoogle Scholar
  30. Casti, J.L. & A. Karlqvist (Editors), 1995. Cooperation and Conflict in General Evolutionary Processes. John Wiley & Sons, Inc., New York.Google Scholar
  31. Cavaillé, J., K. Buiting, M. Kiefmann, M. Lalande, C.I. Brannan et al., 2000. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. P. Natl. Acad. Sci. USA 97: 14311-14316.Google Scholar
  32. Cavaillé, J., P. Vitali, E. Basyuk, A. Hüttenhofer & J.P. Bachellerie, 2001. A novel brain-specific box C/D small nucleolar RNA processed from tandemly repeated introns of a noncoding RNA gene in rats. J. Biol. Chem. 276: 26374-26383.PubMedGoogle Scholar
  33. Cavaillé, J., H. Seitz, M. Paulsen, A.C. Ferguson-Smith & J.P. Bachellerie, 2002. Identification of tandemlyrepeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum. Mol. Genet. 11: 1527-1538.PubMedGoogle Scholar
  34. Chen, W., W. Böcker, J. Brosius & H. Tiedge, 1997a. Expression of neural BC200 RNA in human tumours. J. Pathol. 183: 345-351.PubMedGoogle Scholar
  35. Chen, W., J. Heierhorst, J. Brosius & H. Tiedge, 1997b. Expression of neural BC1 RNA: induction in murine tumours. Eur. J. Cancer. 33: 288-292.PubMedGoogle Scholar
  36. Cheng, J.G., H. Tiedge & J. Brosius, 1996. Identification and characterization of BC1 RNP particles. DNA Cell Biol. 15: 549-559.PubMedGoogle Scholar
  37. Cheng, J.G., H. Tiedge & J. Brosius, 1997. Expression of dendritic BC200 RNA, component of a 11.4S ribonucleoprotein particle, is conserved in humans and simians. Neurosci. Lett. 224: 206-210.PubMedGoogle Scholar
  38. Comeron, J.M., 2001. What controls the length of noncoding DNA? Curr. Opin. Genet. Dev. 11: 652-659.PubMedGoogle Scholar
  39. Copeland, N.G., N.A. Jenkins & S.J. O'Brien, 2002. Genomics. Mmu 16-comparative genomic highlights. Science 296: 1617-1618.PubMedGoogle Scholar
  40. Costas, J., 2002. Characterization of the intragenomic spread of the human endogenous retrovirus family HERV-W. Mol. Biol. Evol. 19: 526-533.PubMedGoogle Scholar
  41. Crick, F.H.C., 1958. On protein synthesis. Sym. Soc. Exp. Biol. 12: 138-183.Google Scholar
  42. Crick, F.H.C., 1970. Central Dogma of Molecular Biology. Nature 227: 561-563.PubMedGoogle Scholar
  43. Davis, S. & J.C. Watson, 1996. In vitro activation of the interferoninduced, double-stranded RNA-dependent protein kinase PKR by RNA from the 3′ untranslated regions of human alphatropomyosin. P. Natl. Acad. Sci. USA 93: 508-513.Google Scholar
  44. Dawkins, R., 1976. The Selfish Gene. Oxford University Press, Oxford, UK.Google Scholar
  45. DeChiara, T.M. & J. Brosius, 1987. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. P. Natl. Acad. Sci. USA 84: 2624-2628.Google Scholar
  46. 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. Prog. Nucleic Acid Re. (edited by W.E. Cohn & K. Moldave) 52: 67-88.Google Scholar
  47. Deloukas, P., L.H. Matthews, J. Ashurst, J. Burton, J.G. Gilbert et al., 2001. The DNA sequence and comparative analysis of human chromosome 20. Nature 414: 865-871.PubMedGoogle Scholar
  48. Devos, K.M., J.K.M. Brown & J.L. Bennetzen, 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079.PubMedGoogle Scholar
  49. Doolittle, W.F., 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.PubMedGoogle Scholar
  50. Eddy, S.R., 2001. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2: 919-929.PubMedGoogle Scholar
  51. Eddy, S.R., 2002. Computational genomics of noncoding RNA genes. Cell 109: 137-140.PubMedGoogle Scholar
  52. Eichler, E.E., 2001a. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 17: 661-669.PubMedGoogle Scholar
  53. Eichler, E.E., 2001b. Segmental duplications: what's missing, misassigned, and misassembled-and should we care? Genome Res. 11: 653-656.PubMedGoogle Scholar
  54. Erdmann, V.A., M.Z. Barciszewska, M. Szymanski, A. Hochberg, N. de Groot et al., 2001. The non-coding RNAs as riboregulators. Nucleic Acids Res. 29: 189-193.PubMedGoogle Scholar
  55. Fagerheim, T., P. Raeymaekers, F.E. Tonnessen, M. Pedersen, L. Tranebjaerg et al., 1999. A new gene (DYX3) for dyslexia is located on chromosome 2. J. Med. Genet. 36: 664-669.PubMedGoogle Scholar
  56. Ferrigno, O., T. Virolle, Z. Djabari, J.P. Ortonne, R.J. White et al., 2001. Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat. Genet. 28: 77-81.PubMedGoogle Scholar
  57. Filipowicz, W., 2000. Imprinted expression of small nucleolar RNAs in brain: time for RNomics. P. Natl. Acad. Sci. USA 97: 14035-14037.Google Scholar
  58. Flavell, A.J., 1995. Retroelements, reverse transcriptase and evolution. Comp. Biochem. Phys. B 110: 3-15.Google Scholar
  59. Gogolevskaya, I.K. & D.A. Kramerov, 2002. Evolutionary history of 4.5SI RNA and indication that it is functional. J. Mol. Evol. 54: 354-364.PubMedGoogle Scholar
  60. Goodier, J.L., E.M. Ostertag & H.H. Kazazian, Jr., 2000. Transduction of 3′-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9: 653-657.PubMedGoogle Scholar
  61. Gould, S.J., 2002. The Structure of Evolutionary Theory. Belknap, Harvard University Press, Cambridge, MA.Google Scholar
  62. Gould, S.J., & E.S. Vrba, 1982. Exaptation-a missing term in the science of form. Paleobiology 8: 4-15.Google Scholar
  63. Herbert, A. & A. Rich, 1999. RNA processing and the evolution of eukaryotes. Nat. Genet. 21: 265-269.PubMedGoogle Scholar
  64. Horike, S., K. Mitsuya, M. Meguro, N. Kotobuki, A. Kashiwagi et al., 2000. Targeted disruption of the human LIT1 locus defines a putative imprinting control element playing an essential role in Beckwith-Wiedemann syndrome. Hum. Mol. Genet. 9: 2075-2083.PubMedGoogle Scholar
  65. Hurst, L.D. & G.T. McVean, 1998. Do we understand the evolution of genomic imprinting? Curr. Opin. Genet. Dev. 8: 701-708.PubMedGoogle Scholar
  66. Hurst, L.D. & N.G. Smith, 1999. Molecular evolutionary evidence that H19 mRNA is functional. Trends Genet. 15: 134-135.PubMedGoogle Scholar
  67. Hurst, L.D., A. Atlan & B.O. Bengtsson, 1996. Genetic conflicts. Q. Rev. Biol. 71: 317-364.PubMedGoogle Scholar
  68. Hüttenhofer, A. & J. Brosius, 2002. Experimental RNomics, pp. 217-240. In Functional Genomics, edited by M. Galperin & E.V. Koonin. Horizon Scientific Press, New York.Google Scholar
  69. Hüttenhofer, A., M. Kiefmann, S. Meier-Ewert, J. O'Brien, H. Lehrach et al., 2001. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20: 2943-2953.PubMedGoogle Scholar
  70. Inouye, S. & M. Inouye, 1995. Structure, function, and evolution of bacterial reverse transcriptase. Virus Genes 11: 81-94.PubMedGoogle Scholar
  71. Iwasa, Y., 1998. The conflict theory of genomic imprinting: how much can be explained? Curr. Top. Dev. Biol. 40: 255-293.PubMedGoogle Scholar
  72. Jamain, S., M. Girondot, P. Leroy, M. Clergue, H. Quach et al., 2001. Transduction of the human gene FAM8A1 by endogenous retrovirus during primate evolution. Genomics 78: 38-45.PubMedGoogle Scholar
  73. Jeffares, D.C., A.M. Poole & D. Penny, 1998. Relics from the RNA world. J. Mol. Evol. 46: 18-36.PubMedGoogle Scholar
  74. Johnson, M.E., L. Viggiano, J.A. Bailey, M. Abdul-Rauf, G. Goodwin et al., 2001. Positive selection of a gene family during the emergence of humans and African apes. Nature 413: 514-519.PubMedGoogle Scholar
  75. Jordan, I.K., L.V. Matyunina & J.F. McDonald, 1999. Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. P. Natl. Acad. Sci. USA 96: 12621-12625.Google Scholar
  76. Jurka, J., 1998. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struc. Biol. 8: 333-337.Google Scholar
  77. 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. P. Natl. Acad. Sci. USA 91: 3607-3611.Google Scholar
  78. Kobayashi, S., S. Goto & K. Anzai, 1991. Brain-specific small RNA transcript of the identifier sequences is present as a 10S ribonucleoprotein particle. J. Biol. Chem. 266: 4726-4730.PubMedGoogle Scholar
  79. Koller, M. & E.E. Strehler, 1988. Characterization of an intronless human calmodulin-like pseudogene. FEBS Lett. 239: 121-128.PubMedGoogle Scholar
  80. Kordis, D. & F. Gubensek, 1998. Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. P. Natl. Acad. Sci. USA 95: 10704-10709.Google Scholar
  81. Kremerskothen, J., M. Nettermann, A. op de Bekke, M. Bachmann & J. Brosius, 1998a. Identification of human autoantigen La/SS-B as BC1/BC200 RNA-binding protein. DNA Cell Biol. 17: 751-759.PubMedGoogle Scholar
  82. Kremerskothen, J., D. Zopf, P. Walter, J.G. Cheng, M. Nettermann et al., 1998b. Heterodimer SRP9/14 is an integral part of the neural BC200 RNP in primate brain. Neurosci Lett. 245: 123-126.PubMedGoogle Scholar
  83. Kurdyukov, S.G., Y.B. Lebedev, Artamonova, II, T.N. Gorodentseva, A.V. Batrak et al., 2001. Full-sized HERVK (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history. Gene 273: 51-61.PubMedGoogle Scholar
  84. Kurychev, V.Y., B.V. Skryabin, J. Kremerskothen, J. Jurka & J. Brosius, 2001. Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage. J. Mol. Biol. 309: 1049-1066.PubMedGoogle Scholar
  85. Lagos-Quintana, M., R. Rauhut, W. Lendeckel & T. Tuschl, 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.PubMedGoogle Scholar
  86. Lagos-Quintana, M., R. Rauhut, A. Yalcin, J. Meyer, W. Lendeckel et al., 2002. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12: 735-739.PubMedGoogle Scholar
  87. Lai, E.C., 2002. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30: 363-364.PubMedGoogle Scholar
  88. Lampson, B.C., S. Inouye & M. Inouye, 1991. msDNA of bacteria. Prog. Nucleic Acid Re. 40: 1-24.Google Scholar
  89. Lau, N.C., L.P. Lim, E.G. Weinstein & D.P. Bartel, 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.PubMedGoogle Scholar
  90. Lee, R.C. & V. Ambros, 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.PubMedGoogle Scholar
  91. Lin, Y., J. Brosius & H. Tiedge, 2001. Neuronal BC1 RNA: coexpression with growth-associated protein-43 messenger RNA. Neuroscience 103: 465-479.PubMedGoogle Scholar
  92. Lipshitz, H.D., D.A. Peattie & D.S. Hogness, 1987. Novel transcripts from the ultrabithorax domain of the bithorax complex. Genes Dev. 1: 307-322.PubMedGoogle Scholar
  93. Liu, A.Y., B.S. Torchia, B.R. Migeon & R.F. Siliciano, 1997. The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics 39: 171-184.PubMedGoogle Scholar
  94. Lottin, S., A.S. Vercoutter-Edouart, E. Adriaenssens, X. Czeszak, J. Lemoine et al., 2002. Thioredoxin post-transcriptional regulation by H19 provides a new function to mRNA-like non-coding RNA. Oncogene 21: 1625-1631.PubMedGoogle Scholar
  95. Lyle, R., D. Watanabe, D. te Vruchte, W. Lerchner, O.W. Smrzka et al., 2000. The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat. Genet. 25: 19-21.PubMedGoogle Scholar
  96. Lyon, M.F., 1998. X-chromosome inactivation: a repeat hypothesis. Cytogenet. Cell Genet. 80: 133-137.PubMedGoogle Scholar
  97. Lyon, M.F., 2000. LINE-1 elements and X chromosome inactivation: a function for 'junk' DNA? P. Natl. Acad. Sci. USA 97: 6248-6249.Google Scholar
  98. Makalowski, W., 2000. Genomic scrap yard: how genomes utilize all that junk. Gene 259: 61-67.PubMedGoogle Scholar
  99. Malik, K., A. Salpekar, A. Hancock, K. Moorwood, S. Jackson et al., 2000. Identification of differential methylation of the WT1 antisense regulatory region and relaxation of imprinting in Wilms' tumor. Cancer Res. 60: 2356-2360.PubMedGoogle Scholar
  100. Martignetti, J.A. & J. Brosius, 1993a. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. P. Natl. Acad. Sci. USA 90: 11563-11567.Google Scholar
  101. Martignetti, J.A. & J. Brosius, 1993b. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent. P. Natl. Acad. Sci. USA 90: 9698-9702.Google Scholar
  102. Martignetti, J.A. & J. Brosius, 1995. BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript. Mol. Cell. Biol. 15: 1642-1650.PubMedGoogle Scholar
  103. Medstrand, P., J.R. Landry & D.L. Mager, 2001. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J. Biol. Chem. 276: 1896-1903.PubMedGoogle Scholar
  104. Meller, V.H. & B.P. Rattner, 2002. The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex. EMBO J. 21: 1084-1091.PubMedGoogle Scholar
  105. Meller, V.H., K.H.Wu, G. Roman, M.I. Kuroda & R.L. Davis, 1997. roX1 RNA paints the X chromosome of male Drosophila and is regulated by the dosage compensation system. Cell 88: 445-457.PubMedGoogle Scholar
  106. Michod, R.E., 1996. Cooperation and conflict in the evolution of individuality. II. Conflict mediation. P. Roy. Soc. Lond. B Bio. 263: 813-822.Google Scholar
  107. Michod, R.E. & D. Roze, 2001. Cooperation and conflict in the evolution of multicellularity. Heredity 86: 1-7.PubMedGoogle Scholar
  108. Millar, J.K., J.C. Wilson-Annan, S. Anderson, S. Christie, M.S. Taylor et al., 2000. Disruption of two novel genes by a translocation co-segregating with schizophrenia. Hum. Mol. Genet. 9: 1415-1423.PubMedGoogle Scholar
  109. Mitsuya, K., M. Meguro, M.P. Lee, M. Katoh, T.C. Schulz et al., 1999. LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids. Hum. Mol. Genet. 8: 1209-1217.PubMedGoogle Scholar
  110. Moore, H., K. Dvorakova, N. Jenkins & W. Breed, 2002. Exceptional sperm cooperation in the wood mouse. Nature 418: 174-177.PubMedGoogle Scholar
  111. Moran, J.V., R.J. DeBerardinis & H.H. Kazazian, Jr., 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530-1534.PubMedGoogle Scholar
  112. Morrish, T.A., N. Gilbert, J.S. Myers, B.J. Vincent, T.D. Stamato et al., 2002. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31: 159-165.PubMedGoogle Scholar
  113. Mouches, C., N. Bensaadi & J.C. Salvado, 1992. Characterization of a LINE retroposon dispersed in the genome of three non-sibling Aedes mosquito species. Gene 120: 183-190.PubMedGoogle Scholar
  114. Muddashetty, R.S., T. Khanam, A. Kondrashov, M. Bundman, A. Iacoangeli e al., 2002. Poly(A) binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J. Mol. Biol. 321: 433-445.PubMedGoogle Scholar
  115. Muller, H.J., A.A. Prokofyeva-Belgovskaya & K.V. Kossikov, 1936. Unequal crossing-over in the Bar mutant as a result of duplication of a minute chromosome section. C. R. (Doklady) Acad. Sci. URSS 1: 87-88.Google Scholar
  116. Mural, R.J., M.D. Adams, E.W. Myers, H.O. Smith, G.L. Miklos et al., 2002. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661-1671.PubMedGoogle Scholar
  117. Muslimov, I.A., G. Banker, J. Brosius & H. Tiedge, 1998. Activitydependent regulation of dendritic BC1 RNA in hippocampal neurons in culture. J. Cell. Biol. 141: 1601-1611.PubMedGoogle Scholar
  118. Muslimov, I.A., Y. Lin, M. Heller, J. Brosius, Z. Zakeri et al., 2002. A small RNA in testis and brain: implications for male germ cell development. J. Cell. Sci. 115: 1243-1250.PubMedGoogle Scholar
  119. Nekrutenko, A. & W.H. Li, 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17: 619-621.PubMedGoogle Scholar
  120. Nemes, J.P., K.A. Benzow, M.L. Moseley, L.P. Ranum & M.D. Koob, 2000. The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). Hum. Mol. Genet. 9: 1543-1551.PubMedGoogle Scholar
  121. Ninomiya, S., M. Isomura, K. Narahara, Y. Seino & Y. Nakamura, 1996. Isolation of a testis-specific cDNA on chromosome 17q from a region adjacent to the breakpoint of t(12;17) observed in a patient with acampomelic campomelic dysplasia and sex reversal. Hum. Mol. Genet. 5: 69-72.PubMedGoogle Scholar
  122. 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
  123. 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
  124. Ohno, S., 1970. Evolution by Gene Duplication. Springer, New York.Google Scholar
  125. Okada, N., 1991. SINEs. Curr. Opin. Genet. Dev. 1: 498-504.PubMedGoogle Scholar
  126. Okada, N., M. Hamada, I. Ogiwara, K. Ohshima, 1997. SINEs and LINEs share common 3′ sequences: a review. Gene 205: 229-243.PubMedGoogle Scholar
  127. Orgel, L.E. & F.H.C. Crick, 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.PubMedGoogle Scholar
  128. Ostertag, E.M. & H.H. Kazazian, Jr., 2001. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35: 501-538.PubMedGoogle Scholar
  129. Paces, J., A. Pavlicek & V. Paces, 2002. HERVd: database of human endogenous retroviruses. Nucleic Acids Res. 30: 205-206.PubMedGoogle Scholar
  130. Parker, G.A. & L. Partridge, 1998. Sexual conflict and speciation. Philos. T. Roy. Soc. B 353: 261-274.Google Scholar
  131. Partridge, L. & L.D. Hurst, 1998. Sex and conflict. Science 281: 2003-2008.PubMedGoogle Scholar
  132. Pasquinelli, A.E., 2002. MicroRNAs: deviants no longer. Trends Genet. 18: 171-173.PubMedGoogle Scholar
  133. Patthy, L., 1991 Exons-original building blocks of proteins? Bioessays 13: 187-192.PubMedGoogle Scholar
  134. Pelczar, P. & W. Filipowicz, 1998. The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5′-terminal oligopyrimidine gene family. Mol. Cell. Biol. 18: 4509-4518.PubMedGoogle Scholar
  135. Petrov, D.A., 2001. Evolution of genome size: new approaches to an old problem. Trends Genet. 17: 23-28.PubMedGoogle Scholar
  136. Petrov, D.A., T.A. Sangster, J.S. Johnston, D.L. Hartl & K.L. Shaw, 2000. Evidence for DNA loss as a determinant of genome size. Science 287: 1060-1062.PubMedGoogle Scholar
  137. Poole, A.M., D.C. Jeffares & D. Penny, 1998. The path from the RNA world. J. Mol. Evol. 46: 1-17.PubMedGoogle Scholar
  138. Quentin, Y., 1994. Emergence of master sequences in families of retroposons derived from 7sl RNA. Genetica 93: 203-215.PubMedGoogle Scholar
  139. Rastinejad, F. & H.M. Blau, 1993. Genetic complementation reveals a novel regulatory role for 3′ untranslated regions in growth and differentiation. Cell 72: 903-917.PubMedGoogle Scholar
  140. Rastinejad, F., M.J. Conboy, T.A. Rando & H.M. Blau, 1993. Tumor suppression by RNA from the 3′ untranslated region of alpha-tropomyosin. Cell 75: 1107-1117.PubMedGoogle Scholar
  141. Renaud, F. & T. de Meeus, 1991. A simple model of host-parasite evolutionary relationships. Parasitism: compromise or conflict? J. Theor. Biol. 152: 319-327.PubMedGoogle Scholar
  142. Rozhdestvensky, T.S., A.M. Kopylov, J. Brosius & A. Hüttenhofer, 2001. Neuronal BC1 RNA structure: evolutionary conversion of a tRNA-Ala domain into an extended stem-loop structure. RNA 7: 722-730.PubMedGoogle Scholar
  143. Runte, M., A. Huttenhofer, S. Gross, M. Kiefmann, B. Horsthemke et al., 2001. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum. Mol. Genet. 10: 2687-2700.PubMedGoogle Scholar
  144. Samonte, R.V. & E.E. Eichler, 2002. Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3: 65-72.PubMedGoogle Scholar
  145. Sawata, M., D. Yoshino, H. Takeuchi, A. Kamikouchi, K. Ohashi et al., 2002. Identification and punctuate nuclear localization of a novel noncoding RNA, Ks-1, from the honeybee brain. RNA 8: 772-785.PubMedGoogle Scholar
  146. Schön, U., W. Seifarth, C. Baust, C. Hohenadl, V. Erfle et al., 2001. Cell type-specific expression and promoter activity of human endogenous retroviral long terminal repeats. Virology 279: 280-291.PubMedGoogle Scholar
  147. Shippen-Lentz, D. & E.H. Blackburn, 1990. Functional evidence for an RNA template in telomerase. Science 247: 546-552.PubMedGoogle Scholar
  148. Skryabin, B.V., J. Kremerskothen, D. Vassilacopoulou, T.R. Disotell, V.V. Kapitonov et al., 1998. The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates). J. Mol. Evol. 47: 677-685.PubMedGoogle Scholar
  149. Skryabin, B.V., V. Sukonina, U. Jordan, N. Sachser & L. Lewejohann, 2003. Role of a small non-messenger RNA in behavior: targeted deletion of neuronal BC1 RNA gene in mice. (submitted).Google Scholar
  150. Sleutels, F., R. Zwart & D.P. Barlow, 2002. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415: 810-813.PubMedGoogle Scholar
  151. Smit, A.F. & A.D. Riggs, 1995. MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res. 23: 98-102.PubMedGoogle Scholar
  152. Sober, E. & D.S. Wilson, 1998. Unto Others. The Evolution and Psychology of Unselfish Behavior. Harvard University Press, Cambridge.Google Scholar
  153. Sorek, R., G. Ast & D. Graur, 2002. Alu-containing exons are alternatively spliced. Genome Res. 12: 1060-1067.PubMedGoogle Scholar
  154. Storz, U., 2002. Counting all genes: how many other RNAs exist and what do they do? Science 296: 1260-1263.PubMedGoogle Scholar
  155. Sturtevant, A.H., 1925. The effects of unequal crossing over at the Bar locus in Drosophila. Genetics 10: 117-147.Google Scholar
  156. Szathmáry, E. & J.M. Smith, 1995. The major evolutionary transitions. Nature 374: 227-232.Google Scholar
  157. Takeda, K., H. Ichijo, M. Fujii, Y. Mochida, M. Saitoh et al., 1998. Identification of a novel bone morphogenetic protein-responsive gene that may function as a noncoding RNA. J. Biol. Chem. 273: 17079-17085.PubMedGoogle Scholar
  158. Taylor, B.A., A. Navin, B.V. Skryabin & J. Brosius, 1997. Localization of the mouse gene (Bc1) encoding neural BC1 RNA near the fibroblast growth factor 3 locus (Fgf3) on distal chromosome 7. Genomics 44: 153-154.PubMedGoogle Scholar
  159. Temin, H.M., 1989. Reverse transcriptases. Retrons in bacteria. Nature 339: 254-255.PubMedGoogle Scholar
  160. Thieffry, D. & S. Sarkar, 1998. Forty years under the central dogma. Trends Biochem. Sci. 23: 312-316.PubMedGoogle Scholar
  161. Tiedge, H., W. Chen & J. Brosius, 1993. Primary structure, neuralspecific expression, and dendritic location of human BC200 RNA. J. Neurosci. 13: 2382-2390.PubMedGoogle Scholar
  162. Tiedge, H., U.C. Dräger & J. Brosius, 1992. Murine BC1 RNA in dendritic fields of the retinal inner plexiform layer. Neurosci. Lett. 141: 136-138.PubMedGoogle Scholar
  163. Tiedge, H., R.T. Fremeau, P.H. Weinstock, O. Arancio & J. Brosius, 1991. Dendritic location of neural BC1 RNA. P. Natl. Acad. Sci. USA 88: 2093-2097.Google Scholar
  164. Tycowski, K.T. & J.A. Steitz, 2001. Non-coding snoRNA host genes in Drosophila: expression strategies for modification guide snoRNAs. Eur. J. Cell. Biol. 80: 119-125.PubMedGoogle Scholar
  165. Tycowski, K.T., M.D. Shu & J.A. Steitz, 1996. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379: 464-466.Google Scholar
  166. Ullu, E. & C. Tschudi, 1984. Alu sequences are processed 7SL RNA genes. Nature 312: 171-172.PubMedGoogle Scholar
  167. Velleca, M.A., M.C. Wallace & J.P. Merlie, 1994. A novel synapse-associated noncoding RNA. Mol. Cell. Biol. 14: 7095-7104.PubMedGoogle Scholar
  168. Vinogradova, T., L. Leppik, E. Kalinina, P. Zhulidov, K.H. Grzeschik et al., 2002. Selective differential display of RNAs containing interspersed repeats: analysis of changes in the transcription of HERV-K LTRs in germ cell tumors. Mol. Genet. Genomics 266: 796-805.PubMedGoogle Scholar
  169. Volff, J.N., C. Korting & M. Schartl, 2000. Multiple lineages of the non-LTR retrotransposon Rex1 with varying success in invading fish genomes. Mol. Biol. Evol. 17: 1673-1684.PubMedGoogle Scholar
  170. Wang, W., F.G. Brunet, E. Nevo & M. Long, 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. P. Natl. Acad. Sci. USA 99: 4448-4453.Google Scholar
  171. Ware, T.L., H. Wang & E.H. Blackburn, 2000. Three telomerases with completely non-telomeric template replacements are catalytically active. EMBO J. 19: 3119-3131.PubMedGoogle Scholar
  172. Watanabe, Y. & M. Yamamoto, 1994. S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78: 487-498.CrossRefPubMedGoogle Scholar
  173. Weiner, A.M., 2002. SINEs and LINEs: the art of biting the hand that feeds you. Curr. Opin. Cell. Biol. 14: 343-350.PubMedGoogle Scholar
  174. Weiner, A.M., P.L. Deininger & A. Efstratiadis, 1986. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55: 631-661.PubMedGoogle Scholar
  175. West, N.C., A.M. Roy-Engel, H. Imataka, N. Sonenberg & P.L. Deininger, 2002. Shared protein components of SINE RNPs. J. Mol. Biol. 321: 423-432.PubMedGoogle Scholar
  176. Williams, G.C., 1997. The Pony Fish's Glow. And Other Clues to Plan and Purpose in Nature. Basic Books, New York, N.Y.Google Scholar
  177. Woese, C.R., 1967. The Genetic Code: The Molecular Basis for Genetic Expression. Harper and Row, New York.Google Scholar
  178. Woese, C.R., 2002. On the evolution of cells. P. Natl. Acad. Sci. USA 99: 8742-8747.Google Scholar
  179. Yamamoto, M., 1996. Regulation of meiosis in fission yeast. Cell Struct. Funct. 21: 431-436.PubMedGoogle Scholar
  180. Yamashita, A., Y. Watanabe, N. Nukina & M. Yamamoto, 1998. RNA-assisted nuclear transport of the meiotic regulator Mei2p in fission yeast. Cell 95: 115-123.PubMedGoogle Scholar
  181. Yaswen, P., A. Smoll, J. Hosoda, G. Parry & M.R. Stampfer, 1992. Protein product of a human intronless calmodulinlike gene shows tissue-specific expression and reduced abundance in transformed cells. Cell Growth Differ. 3: 335-345.PubMedGoogle Scholar
  182. Zupunski, V., F. Gubensek & D. Kordis, 2001. Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol. Biol. Evol. 18: 1849-1863.PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Jürgen Brosius
    • 1
  1. 1.Institute of Experimental Pathology, ZMBEUniversity of MünsterMünsterGermany

Personalised recommendations