Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins

Molecular Biology and Evolution

Volumn 19, Issue 11, 2002, Pages 1964-1972

  Nishihara, Hidenori ^a   Terai, Yohey ^a   Okada, Norihiro ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

7SL RNA; Alu; Retroposon; SRP; Tree shrew; tRNA

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; TRANSFER RNA;

ALU SEQUENCE; ARTICLE; ENZYME ANALYSIS; GENETIC CONSERVATION; HOST SELECTION; INTERSPECIFIC RELATIONSHIP; MOLECULAR EVOLUTION; MOLECULAR HYBRIDIZATION; MOLECULAR STABILITY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; PROMOTER REGION; PROSIMIAN; PROTEIN DOMAIN; RNA ANALYSIS; RNA HYBRIDIZATION; RODENT; SHORT INTERSPERSED REPEAT; SPECIES DIFFERENCE; STRUCTURE ANALYSIS; ANIMAL; CHEMISTRY; CONFORMATION; GENETICS; MOLECULAR GENETICS; SCANDENTIA;

GALAGO; PRIMATES; RODENTIA; STREPSIRHINI; TUPAIA BELANGERI; TUPAIA GLIS;

ALU ELEMENTS; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; PHYLOGENY; PRIMATES; RNA, TRANSFER; RODENTIA; TUPAIIDAE;

EID: 0036854336     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004020     Document Type: Article

References (41)

1. Batzer, M. A., C. W. Schmid, and P. L. Deininger. 1993. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol. 224:213-232.
2. Borodulina, O. R., and D. A. Kramerov. 1999. Wide distribution of short interspersed elements among eukaryotic genomes. FEBS Lett. 457:409-413.
3. Daniels, G. R., and P. L. Deininger. 1983. A second major class of Alu family repeated DNA sequences in a primate genome. Nucleic Acids Res. 11:7595-7610.
4. -. 1991. Characterization of a third major SINE family of repetitive sequences in the galago genome. Nucleic Acids Res. 19:1649-1656.
5. Eickbush, T. H. 1994. Origin and evolutionary relationships of retroelements. Pp. 121-157 in S. S. Morse, ed. The Evolutionary Biology of Viruses. Raven Press, New York.
6. Endoh, H., S. Nagahashi, and N. Okada. 1990. A highly repetitive and transcribable sequence in the tortoise genome is probably a retroposon. Eur. J. Biochem. 189:25-31.
7. Endoh, H., and N. Okada. 1986. Total Dna transcription in vitro: A procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc. Natl. Acad. Sci. USA 83:251-255.
8. Fanning, T. G., and M. F. Singer. 1987. Line-I: A mammalian transposable element. Biochem. Biophys. Acta 910:203-212.
9. Gauss, D. H., F. Grüter, and M. Sprinzl. 1979. Compilation of tRNA sequences. Pp. 518-537 in J. N. Abelson, ed. Transfer RNA: Structure, Properties, and Recognition. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
10. Gundelfinger, E. D., E. Krause, M. Melli, and B. Dobberstein. 1983. The organization of the 7SL RNA in the signal recognition particle. Nucleic Acids Res. 11:7363-7374.
11. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
12. Jagadeeswaran, P., B. G. Forget, and S. M. Weissman. 1981. Short interspersed repetitive DNA elements in eucaryotes: Transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell 26:141-142.
13. Jurka, J., and E. Zuckerkandl. 1991. Free left arms as precursor molecules in the evolution of Alu sequences. J. Mol. Evol. 33:49-56.
14. Kido, Y., M. Aono, T. Yamaki, K. Matsumoto, S. Murata, M. Saneyoshi, and N. Okada. 1991. Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. Proc. Natl. Acad. Sci. USA 88:2326-2330.
15. Labuda, D., and E. Zietkiewicz. 1994. Evolution of secondary structure in the family of 7SL-like RNAs. J. Mol. Evol. 39:506-518.
16. Lutcke, H. 1995. Signal recognition particle (SRP), a ubiquitous initiator of protein translocation. Eur. J. Biochem. 228:531-550.
17. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, R. W. Debry, R. Adkins, H. M. Amrine, M. J. Stanhope, W. W. De Jong, and M. S. Springer. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
18. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
19. Murphy, W. J., E. Eizirik, S. J. O'Brien et al. (11 co-authors). 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
20. Ohshima, K., R. Koishi, M. Matsuo, and N. Okada. 1993. Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: Characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons. Proc. Natl. Acad. Sci. USA 90:6260-6264.
21. Okada, N. 1991a. SINEs. Curr. Opin. Genet. Dev. 1:498-504.
22. -. 1991b. SINEs: Short interspersed repeated elements of the eucaryotic genome. Trends Ecol. Evol. 6:358-361.
23. Okada, N., and K. Ohshima. 1995. Evolution of tRNA-derived SINEs. Pp. 61-79 in R. J. Maraia, eds. The Impact of Short Interspersed Elements (SINEs) on the Host Genome. R. G. Landes, Austin, Tex.
24. Quentin, Y. 1992a. 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.
25. -. 1992b. Origin of the Alu family: A family of Alu-like monomers gave birth to the left and the right arms of the Alu elements. Nucleic Acids Res. 20:3397-3401.
26. -. 1994. A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes. Nucleic Acids Res. 22:2222-2227.
27. Rogers, J. H. 1985. Long interspersed sequences in mammalian DNA. Properties of newly identified specimens. Biochem. Biophys. Acta 824:113-120.
28. Sakamoto, K., and N. Okada. 1985. Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J. Mol. Biol. 22:134-140.
29. Schmid, C., and R. Maraia. 1992. Transcriptional regulation and transpositional selection of active SINE sequences. Curr. Opin. Genet. Dev. 2:874-882.
30. Shedlock, A. M., and N. Okada. 2000. SINE insertions: Powerful tools for molecular systematics. Bioessays 22:148-160.
31. Singer, M., and P. Berg. 1991. Genes & Genomes. University Science Books, Mill Valley, Calif.
32. Smit, A. E, and A. D. Riggs. 1995. MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res. 23:98-102.
33. Smit, A. F., G. Toth, A. D. Riggs, and J. Jurka. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246:401-417.
34. Takahashi, K., Y. Terai, M. Nishida, and N. Okada. 1998. A novel family of short interspersed repetitive elements (SINEs) from cichlids: The patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika. Mol. Biol. Evol. 15:391-407.
35. Ullu, E., and C. Tschudi. 1984. Alu sequences are processed 7SL RNA genes. Nature 312:171-172.
36. Van Arsdell, S. W., R. A. Denison, L. B. Bernstein, A. M. Weiner, T. Manser, and R. F. Gesteland. 1981. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell 26:11-17.
37. Walter, P., and A. E. Johnson. 1994. Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. Annu. Rev. Cell Biol. 10:87-119.
38. Weichenrieder, O., K. Wild, K. Strub, and S. Cusack. 2000. Structure and assembly of the Alu domain of the mammalian signal recognition particle. Nature 408:167-173.
39. Weiner, A. M. 1980. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22:209-218.
40. Weiner, A. M., P. L. Deininger, and A. Efstratiadis. 1986. Nonviral retroposons: Genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55:631-661.
41. Willis, I. M. 1993. RNA polymerase III. Genes, factors and transcriptional specificity. Eur. J. Biochem. 212:1-11.