A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus)

Molecular Biology and Evolution

Volumn 22, Issue 4, 2005, Pages 886-893

  Churakov, Gennady ^a   Smit, Arian F A ^b   Brosius, Jürgen ^a   Schmitz, Jürgen ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Armadillo; Retroposition; SINE; SINE evolution; tRNA

Indexed keywords

DIMER; GENE PRODUCT; MONOMER; TRANSFER RNA;

ALGORITHM; ARMADILLO; ARTICLE; CONSENSUS SEQUENCE; DASYPUS NOVEMCINCTUS; DIMERIZATION; EDENTATA; GENE DELETION; GENE INSERTION; GENE MUTATION; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME ANALYSIS; LONG INTERSPERSED REPEAT; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE REPEAT; RETROPOSON; RNA EXTRACTION; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SHORT INTERSPERSED REPEAT;

ANIMALS; ARMADILLOS; BASE SEQUENCE; DNA PRIMERS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RETROELEMENTS; RNA, TRANSFER, ALA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; SPECIES SPECIFICITY;

EID: 16344366343     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi071     Document Type: Article

References (42)

1. Batzer, M. A., P. L. Deininger, U. Hellmann-Blumberg, J. Jurka, D. Labuda, C. M. Rubin, C. W. Schmid, E. Zietkiewicz, and E. Zuckerkandl. 1996. Standardized nomenclature for Alu repeats. J. Mol. Evol. 42:3-6.
2. Bentolila, S., J. M. Bach, J. L. Kessler, I. Bordelais, C. Cruaud, J. Weissenbach, and J. J. Panthier. 1999. Analysis of major repetitive DNA sequences in the dog (Canis familiaris) genome. Mamm. Genome 10:699-705.
3. Borodulina, O. R., and D. A. Kramerov. 2001. Short interspersed elements (SINEs) from insectivores: two classes of mammalian SESIEs distinguished by A-rich tail structure. Mamm. Genome 12:779-786.
4. Brosius, J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134.
5. Brosius, J., and 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.
6. Buzdin, A. A. 2004. Retroelements and formation of chimeric retrogenes. Cell. Mol. Life Sci. 61:1-14.
7. Cheng, J. F., R. Printz, T. Callaghan, D. Shuey, and R. C. Hardison. 1984. The rabbit C family of short, interspersed repeats: nucleotide sequence determination and transcriptional analysis. J. Mol. Biol. 176:1-20.
8. Cost, G. J., Q. Feng, A. Jacquier, and J. D. Boeke. 2002. Human L1 element target-primed reverse transcription in vitro. EMBO J. 21:5899-5910.
9. Daniels, G. R., and P. L. Deininger. 1991. Characterization of a third major SINE family of repetitive sequences in the galago genome. Nucleic Acids Res. 19:1649-1656.
10. Dewannieux, M., C. Esnault, and T. Heidmann. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35:41-48.
11. Feschotte, C., N. Fourrier, I. Desmons, and C. Mouches. 2001. Birth of a retroposon: the twin sine family from the vector mosquito Culex pipiens may have originated from a dimeric tRNA precursor. Mol. Biol. Evol. 18:74-84.
12. Gilbert, N., and D. Labuda. 2000. Evolutionary inventions and continuity of CORE-SINEs in mammals. J. Mol. Biol. 298:365-377.
13. Hagan, R., F. Sheffield, and C. M. Rudin. 2003. Human Alu element retroposition induced by genotoxic stress. Nat. Genet. 35:219-220.
14. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
15. Jurka, J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94:1872-1877.
16. Kajikawa M., and N. Okada. 2002. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111:433-444.
17. Kapitonov, V. V., and J. Jurka. 2003. A novel class of SINE elements derived from 5S rRNA. Mol. Biol. Evol. 20:694-702.
18. Kapitonov, V. V., A. Pavlicek, and J. Jurka. 2004. Anthology of human repetitive DNA. Pp. 251-306 in R. A. Meyers, ed. Encyclopedia of molecular cell biology and molecular medicine, Vol. 1. Wiley VCH, Weinheim, Germany.
19. Kass, D. H., J. Kim, and P. L. Deininger. 1996. Sporadic amplification of ID elements in rodents. J. Mol. Evol. 42:7-14.
20. Katoh, K., K. Misawa, K. Kuma, and T. Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.
21. Kramerov, D. A., A. A. Grigoryan, A. P. Ryskov, and G. P. Georgiev. 1979. Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res. 6:697-713.
22. Lander, E. S., L. M. Linton, B. Birren, et al. (256 co-authors) 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
23. Lin, Z., O. Nomura, T. Hayashi, Y. Wada, and H. Yasue. 2001. Characterization of a SINE species from vicuna and its distribution in animal species including the family Camelidae. Mamm. Genome 12:305-308.
24. Mak, J., and L. Kleiman. 1997. Primer tRNAs for reverse transcription. J. Virol. 71:8087-8095.
25. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
26. Nikaido, M., H. Nishihara, Y. Hukumoto, and N. Okada. 2003. Ancient SINEs from African endemic mammals. Mol. Biol. Evol. 20:522-527.
27. Nikaido, M., A. P. Rooney, and N. Okada. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. USA 96:10261-10266.
28. Nishihara, H., Y. Terai, and N. Okada. 2002. Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins. Mol. Biol. Evol. 19:1964-1972.
29. Ohshima, K., M. Hamada, Y. Terai, and 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.
30. Okada, N., and K. Ohshima. 1995. Evolution of tRNA-derived SINEs. Pp. 61-79 in R. J. Maraia, ed. The impact of short interspersed elements (SINEs) on the host genome. RG Landes Company, Austin, Tex.
31. Piskurek, O., M. Nikaido, Boeadi, M. Baba, and N. Okada. 2003. Unique mammalian tRNA-derived repetitive elements in Dermopterans: The t-SINE family and its retrotransposition through multiple sources. Mol. Biol. Evol. 20:1659-1668.
32. Quentin, Y. 1992. Fusion of a free left Alu monomer and a free right Alu monomer at the origin of the Alu family in the primate genomes. Nucleic Acids Res. 20:487-493.
33. Rogers, J. H. 1985. The origin and evolution of retroposons. Int. Rev. Cytol. 93:187-279.
34. Roos, C., J. Schmitz, and H. Zischler. 2004. Primate jumping genes elucidate strepsirrhine phylogeny. Proc. Natl. Acad. Sci. USA 101:10650-10654.
35. Rozhdestvensky, T. S., A. M. Kopylov, J. Brosius, and A. Huttenhofer. 2001. Neuronal BC1 RNA structure: evolutionary conversion of a tRNA(Ala) domain into an extended stem-loop structure. RNA 7:722-730.
36. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
37. Schmitz, J., G. Churakov, H. Zischler, and J. Brosius. 2004. A novel class of mammalian-specific tailless retropseudogenes. Genome Res. 14:1911-1915.
38. Schmitz, J., and H. Zischler. 2003. A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates. Mol. Phylogenet. Evol. 28:341-349.
39. Shimamura, M., H. Yasue, K. Ohshima, H. Abe, H. Kato, T. Kishiro, M. Goto, I. Munechika, and N. Okada. 1997. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388:666-670.
40. Szemraj, J., G. Plucienniczak, J. Jaworski, and A. Plucienniczak. 1995. Bovine Alu-like sequences mediate transposition of a new site-specific retroelement. Gene 152:261-264.
41. Ullu, E., and C. Tschudi. 1984. Alu sequences are processed 7SL RNA genes. Nature 312:171-172.
42. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.