Modern genomes with retro-look: Retrotransposed elements, retroposition and the origin of new genes

Genome Dynamics

Volumn 3, Issue , 2007, Pages 175-190

  Volff, J N ^a   Brosius, J ^b  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICRORNA; RNA DIRECTED DNA POLYMERASE; SMALL NUCLEOLAR RNA; TELOMERASE; UBIQUINOL CYTOCHROME C REDUCTASE; RNA;

ALU SEQUENCE; CONTROLLED STUDY; DNA TRANSPOSITION; ENDOGENOUS RETROVIRUS; ENVELOPE GENE; GENE DUPLICATION; GENE FUNCTION; GENOME; HUMAN; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NERVE CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIMATE; PRIORITY JOURNAL; RETROPOSON; REVIEW; RNA GENE; RNA TRANSCRIPTION; STRUCTURAL GENE; ANIMAL; GENETICS; OPEN READING FRAME;

ANIMALIA; MAMMALIA; PRIMATES; RODENTIA;

ALU ELEMENTS; ANIMALS; EVOLUTION, MOLECULAR; GENOME; HUMANS; OPEN READING FRAMES; RETROELEMENTS; RNA;

EID: 38549180414     PISSN: 16609263     EISSN: None     Source Type: Book Series    
DOI: 10.1159/000107611     Document Type: Review

References (76)

1. Orgel LE, Crick FH: Selfish DNA: the ultimate parasite. Nature 1980;284:604-607.
2. Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999;238:115-134.
3. Kazazian HH Jr: Mobile elements: drivers of genome evolution. Science 2004;303:1626-1632.
4. Nekrutenko A, Li WH: Transposable elements are found in a large number of human protein-coding genes. Trends Genet 2001;17:619-621.
5. Gotea V, Makalowski W: Do transposable elements really contribute to proteomes? Trends Genet 2006;22:260-267.
6. Krull M, Brosius J, Schmitz J: Alu-SINE exonization: en route to protein-coding function. Mol Biol Evol 2005;22:1702-1711.
7. Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK: Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet Genome Res 2005;110:333-341.
8. Debarry JD, Ganko EW, McCarthy EM, McDonald JF: The contribution of LTR retrotransposon sequences to gene evolution in Mus musculus. Mol Biol Evol 2006;23:479-481.
9. Deininger PL, Moran JV, Batzer MA, Kazazian HH Jr: Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 2003;13:651-658.
10. Volff JN: Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 2006;28:913-922.
11. Brandt J, Schrauth S, Veith AM, Froschauer A, Haneke T, et al: Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. Gene 2004;345:101-111.
12. Youngson NA, Kocialkowski S, Peel N, Ferguson-Smith AC: A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. J Mol Evol 2005;61:481-490.
13. Poulter R, Butler M: A retrotransposon family from the pufferfish (fugu) Fugu rubripes. Gene 1998;215:241-249.
14. Wills NM, Moore B, Hammer A, Gesteland RF, Atkins JF: A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. J Biol Chem 2006;281:7082-7088.
15. Nagasaki K, Schem C, von Kaisenberg C, Biallek M, Rosel F, et al: Leucine-zipper protein, LDOC1, inhibits NF-kappaB activation and sensitizes pancreatic cancer cells to apoptosis. Int J Cancer 2003;105:454-458.
16. Tan KO, Tan KM, Chan SL, Yee KS, Bevort M, et al: MAP-1, a novel proapoptotic protein containing a BH3-like motif that associates with Bax through its Bcl-2 homology domains. J Biol Chem 2001;276:2802-2807.
17. Ono R, Nakamura K, Inoue K, Naruse M, Usami T, et al: Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality. Nat Genet 2006;38:101-106.
18. Seitz H, Youngson N, Lin SP, Dalbert S, Paulsen M, et al: Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet 2003;34:261-262.
19. Best S, Le Tissier P, Towers G, Stoye JP: Positional cloning of the mouse retrovirus restriction gene Fv1. Nature 1996;382:826-829.
20. Campillos M, Doerks T, Shah PK, Bork P: Computational characterization of multiple Gag-like human proteins. Trends Genet 2006;22:585-589.
21. Llorens C, Marin I: A mammalian gene evolved from the integrase domain of an LTR retrotransposon. Mol Biol Evol 2001;18:1597-1600.
22. Dlakic M: A model of the replication fork blocking protein Fob1p based on the catalytic core domain of retroviral integrases. Protein Sci 2002;11:1274-1277.
23. Mi S, Lee X, Li X, Veldman GM, Finnerty H, et al: Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 2000;403:785-789.
24. Blaise S, de Parseval N, Benit L, Heidmann T: Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc Natl Acad Sci USA 2003;100:13013- 13018.
25. Dupressoir A, Marceau G, Vernochet C, Benit L, Kanellopoulos C, et al: Syncytin-A and syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae. Proc Natl Acad Sci USA 2005;102:725-730.
26. Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, et al: Endogenous retroviruses regulate periimplantation placental growth and differentiation. Proc Natl Acad Sci USA 2006;103:14390-14395.
27. Malik HS, Henikoff S: Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PLoS Genet 2005;1:e44.
28. Nakamura TM, Cech TR: Reversing time: origin of telomerase. Cell 1998;92:587-590.
29. Eickbush TH: Telomerase and retrotransposons: which came first? Science 1997;277:911-912.
30. Brosius J: Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet 1999;15:304-305.
31. Vinckenbosch N, Dupanloup I, Kaessmann H: Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 2006;103:3220-3225.
32. Brosius J: Retroposons - seeds of evolution. Science 1991;251:753.
33. Betran E, Thornton K, Long M: Retroposed new genes out of the X in Drosophila. Genome Res 2002;12:1854-1859.
34. Emerson JJ, Kaessmann H, Betran E, Long M: Extensive gene traffic on the mammalian X chromosome. Science 2004;303:537-540.
35. Bradley J, Baltus A, Skaletsky H, Royce-Tolland M, Dewar K, Page DC: An X-to-autosome retrogene is required for spermatogenesis in mice. Nat Genet 2004;36:872-876.
36. Brosius J, Gould SJ: On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA'. Proc Natl Acad Sci USA 1992;89:10706-10710.
37. Brosius J: Echoes from the past - are we still in an RNP world? Cytogenet Genome Res 2005;110:8-24.
38. Brosius J: More Haemophilus and Mycoplasma genes. Science 1996;271:1302.
39. Ambros V: microRNAs: tiny regulators with great potential. Cell 2001;107:823-826.
40. Mattick JS, Makunin IV: Non-coding RNA. Hum Mol Genet 2006;15(spec 1):R17-R29.
41. Sutcliffe JG, Milner RJ, Gottesfeld JM, Lerner RA: Identifier sequences are transcribed specifically in brain. Nature 1984;308:237-241.
42. DeChiara TM, Brosius J: Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc Natl Acad Sci USA 1987;84:2624-2628.
43. Kim J, Martignetti JA, Shen MR, Brosius J, Deininger P: Rodent BC1 RNA gene as a master gene for ID element amplification. Proc Natl Acad Sci USA 1994;91:3607-3611.
44. Kim J, Deininger PL: Recent amplification of rat ID sequences. J Mol Biol 1996;261:322-327.
45. Martignetti JA, Brosius J: BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript. Mol Cell Biol 1995;15:1642-1650.
46. Tiedge H, Fremeau RT Jr, Weinstock PH, Arancio O, Brosius J: Dendritic location of neural BC1 RNA. Proc Natl Acad Sci USA 1991;88:2093-2097.
47. Rozhdestvensky TS, Kopylov AM, Brosius J, Huttenhofer A: Neuronal BC1 RNA structure: evolutionary conversion of a tRNA(Ala) domain into an extended stem-loop structure. RNA 2001;7:722-730.
48. Muslimov IA, Iacoangeli A, Brosius J, Tiedge H: Spatial codes in dendritic BC1 RNA. J Cell Biol 2006;175:427-439.
49. Muslimov IA, Banker G, Brosius J, Tiedge H: Activity-dependent regulation of dendritic BC1 RNA in hippocampal neurons in culture. J Cell Biol 1998;141:1601-1611.
50. Chen W, Heierhorst J, Brosius J, Tiedge H: Expression of neural BC1 RNA: induction in murine tumours. Eur J Cancer 1997;33:288-292.
51. Muddashetty R, Khanam T, Kondrashov A, Bundman M, Iacoangeli A, et al: Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J Mol Biol 2002;321:433-445.
52. Kondrashov AV, Kiefmann M, Ebnet K, Khanam T, Muddashetty RS, Brosius J: Inhibitory effect of naked neural BC1 RNA or BC200 RNA on eukaryotic in vitro translation systems is reversed by poly(A)-binding protein (PABP). J Mol Biol 2005;353:88-103.
53. Kindler S, Wang H, Richter D, Tiedge H: RNA transport and local control of translation. Annu Rev Cell Dev Biol 2005;21:223-245.
54. Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P, et al: Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav Brain Res 2004;154:273-289.
55. Watson JB, Sutcliffe JG: Primate brain-specific cytoplasmic transcript of the Alu repeat family. Mol Cell Biol 1987;7:3324-3327.
56. Skryabin BV, Kremerskothen J, Vassilacopoulou D, Disotell TR, Kapitonov VV, et al: The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates). J Mol Evol 1998;47:677-685.
57. Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J: Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 2007;23:153-161.
58. Shen MR, Batzer MA, Deininger PL: Evolution of the master Alu gene(s). J Mol Evol 1991;33:311-320.
59. Jurka J, Milosavljevic A: Reconstruction and analysis of human Alu genes. J Mol Evol 1991;32:105-121.
60. Kuryshev VY, Skryabin BV, Kremerskothen J, Jurka J, Brosius J: 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 2001;309:1049-1066.
61. Tiedge H, Chen W, Brosius J: Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. J Neurosci 1993;13:2382-2390.
62. Chen W, Bocker W, Brosius J, Tiedge H: Expression of neural BC200 RNA in human tumours. J Pathol 1997;183:345-351.
63. Bovia F, Wolff N, Ryser S, Strub K: The SRP9/14 subunit of the human signal recognition particle binds to a variety of Alu-like RNAs and with higher affinity than its mouse homolog. Nucleic Acids Res 1997;25:318-326.
64. Kremerskothen J, Zopf D, Walter P, Cheng JG, Nettermann M, et al: Heterodimer SRP9/14 is an integral part of the neural BC200 RNP in primate brain. Neurosci Lett 1998;245:123-126.
65. Ludwig A, Rozhdestvensky TS, Kuryshev VY, Schmitz J, Brosius J: An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J Mol Biol 2005;350:200-214.
66. Khanam T, Rozhdestvensky TS, Bundman M, Galiveti CR, Handel S, et al: Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners. Nucleic Acids Res 2007;35:529-539.
67. Leverette RD, Andrews MT, Maxwell ES: Mouse U14 snRNA is a processed intron of the cognate hsc70 heat shock pre-messenger RNA. Cell 1992;71:1215-1221.
68. Tycowski KT, Shu MD, Steitz JA: A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. Genes Dev 1993;7:1176-1190.
69. Balakin AG, Smith L, Fournier MJ: The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 1996;86:823-834.
70. Brosius J: The contribution of RNAs and retroposition to evolutionary novelties. Genetica 2003;118:99-116.
71. Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J: Identification of 13 novel human modification guide RNAs. Nucleic Acids Res 2003;31:6543-6551.
72. Luo Y, Li S: Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs. Nucleic Acids Res 2007;35:559-571.
73. Weber MJ: Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet 2006;2:e205.
74. Kiss T, Filipowicz W: Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev 1995;9:1411-1424.
75. Houbaviy HB, Dennis L, Jaenisch R, Sharp PA: Characterization of a highly variable eutherian microRNA gene. RNA 2005;11:1245-1257.
76. Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, et al: Diversity of microRNAs in human and chimpanzee brain. Nat Genet 2006;38:1375-1377.