Retroposed SNOfall - A mammalian-wide comparison of platypus snoRNAs

Genome Research

Volumn 18, Issue 6, 2008, Pages 1005-1010

  Schmitz, Jürgen ^a   Zemann, Anja ^a   Churakov, Gennady ^a   Kuhl, Heiner ^b   Grützner, Frank ^c   Reinhardt, Richard ^b   Brosius, Jürgen ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b MPI Molecular Genetics   (Germany)

^c UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL NUCLEOLAR RNA;

ARTICLE; COMPARATIVE STUDY; EVOLUTION; GENE DUPLICATION; GENETIC TRANSCRIPTION; HOUSEKEEPING GENE; MAMMAL; NEMATODE; NONHUMAN; PLATYPUS; PRIORITY JOURNAL; PROMOTER REGION; RETROPOSON; VERTEBRATE;

ANIMALS; GENE DUPLICATION; MALE; MAMMALS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLATYPUS; RETROELEMENTS; RNA, SMALL NUCLEOLAR;

EUKARYOTA; MAMMALIA; MONOTREMATA; NEMATODA; ORNITHORHYNCHUS ANATINUS; TACHYGLOSSIDAE; VERTEBRATA;

EID: 43749105204     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.7177908     Document Type: Article

References (25)

1. Cavaillé, J. and Bachellerie, J.-P. 1996. Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: An exonucleolytic process exclusively directed by the common stem-box terminal structure. Biochimie 78: 443-456.
2. Chen, X.S., Rozhdestvensky, T.S., Collins, L.J., Schmitz, J., and Penny, D. 2007. Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res. 35: 4619-4628.
3. DeChiara, T.M. and Brosius, J. 1987. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc. Natl. Acad. Sci. 84: 2624-2628.
4. Gentles, A.J., Wakefield, M.J., Kohany, O., Gu, W., Batzer, M.A., Pollock, D.D., and Jurka, J. 2007. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. 17: 992-1004.
5. Gogolevsky, K.P., Vassetzky, N.S., and Kramerov, D.A. 2007. Bov-B-mobilized SINEs in vertebrate genomes. Gene 407: 75-85.
6. Katoh, K., Misawa, K., Kuma, K.-I., and Miyata, T. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066.
7. Khanam, T., Rozhdestvensky, T.S., Bundman, M., Galiveti, C.R., Handel, S., Sukonina, V., Jordan, U., Brosius, J., and Skryabin, B.V. 2007. Two primate-specific small non-protein-coding RNAs in transgenic mice: Neuronal expression, subcellular localization and binding partners. Nucleic Acids Res. 35: 529-539.
8. Kordis, D., Lovsin, N., and Gubensek, F. 2006. Phylogenomic analysis of the L1 retroposons in Deuterostomia. Syst. Biol. 55: 886-901.
9. Kriegs, J.O., Churakov, G., Kiefmann, M., Jordan, U., Brosius, J., and Schmitz, J. 2006. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol. 4: e91. doi: 10.1371/journal. pbio.0040091.
10. Krull, M., Petrusma, M., Makalowski, W., Brosius, J., and Schmitz, J. 2007. Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). Genome Res. 17: 1139-1145.
11. Long, M., Betran, E., Thornton, K., and Wang, W. 2003. The origin of new genes: Glimpses from the young and old. Nat. Rev. Genet. 4: 865-875.
12. Ludwig, A., Rozhdestvensky, T.S., Kuryshev, V.Y., Schmitz, J., and Brosius, J. 2005. An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J. Mol. Biol. 350: 200-214.
13. Luo, Y. and Li, S. 2007. Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs. Nucleic Acids Res. 35: 559-571.
14. Malik, H.S. and Eickbush, T.H. 1998. The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol. Biol. Evol. 15: 1123-1134.
15. Okada, N. and Hamada, M. 1997. The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: A new example from the bovine genome. J. Mol. Evol. 44: S052-S056.
16. Pasyukova, E.G., Nuzhdin, S.V., Morozova, T.V., and Mackay, T.F. 2004. Accumulation of transposable elements in the genome of Drosophila melanogaster is associated with a decrease in fitness. J. Hered. 95: 284-290.
17. Piskurek, O. and Okada, N. 2007. Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc. Natl. Acad. Sci. 104: 12046-12051.
18. Schmitz, J., Churakov, G., Zischler, H., and Brosius, J. 2004. A novel class of mammalian-specific tailless retropseudogenes. Genome Res. 14: 1911-1915.
19. Tanzer, A. and Stadler, P.F. 2006. Evolution of microRNAs. Methods Mol. Biol. 342: 335-350.
20. Vitali, P., Royo, H., Seitz, H., Bachellerie, J.P., Hüttenhofer, A., and Cavaille, J. 2003. Identification of 13 novel human modification guide RNAs. Nucleic Acids Res. 31: 6543-6551.
21. Weber, M.J. 2006. Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet. 3: e36. doi: 10.1371/journal.pgen.0020205.
22. Xing, Y. and Lee, C. 2006. Alternative splicing and RNA selection pressure evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 7: 499-509.
23. Youngman, S., van Luenen, H.G.A.M., and Plasterk, R.H.A. 1996. Rte-1, a retrotransposon-like element in Caenorhabditis elegans. FEBS Lett. 380: 1-7.
24. Zemann, A., op de Bekke, A., Kiefmann, M., Brosius, J., and Schmitz, J. 2006. Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 34: 2676-2685.
25. Zupunski, V., Gubensek, F., and Kordis, D. 2001. Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol. Biol. Evol. 18: 1849-1863.