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LINE-mediated retrotransposition of marked Alu sequences

Nature Genetics volume 35, pages 41–48 (2003)Cite this article

Abstract

Alu elements are the most successful transposons in humans. They are 300-bp non-coding sequences transcribed by RNA polymerase III (Pol III) and are expected to retrotranspose with the aid of reverse transcriptases of cellular origin. We previously showed that human LINEs can generate cDNA copies of any mRNA transcript by means of a retroposition process involving reverse transcription and integration by the LINE-encoded endonuclease and reverse transcriptase. Here we show mobility of marked Alu sequences in human HeLa cells with the canonical features of a retrotransposition process, including splicing out of an autocatalytic intron introduced into the marked sequence, target site duplications of varying lengths and integrations into consensus A-rich sequences. We further show that the poly-A stretch at the Alu 3′ end is essential for mobility, that LINEs are required for transposition and that the rate of retroposition is 100–1,000 times higher for Alu transcripts than for control mRNAs, thus accounting for the high mutational activity of these elements observed in humans.

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Figure 1: Structure of the Alu SINE and rationale of the assay for retrotransposition.
Figure 2: High frequency L1-mediated Alu retrotransposition.
Figure 3: Structure of retrotransposed marked Alu sequences.
Figure 4: Chromosomal localization and properties of five de novo marked Alu insertions.
Figure 5: Elements required in trans for Alu retrotransposition.
Figure 6: Alu sequences required in cis for retrotransposition: role of the Alu poly-A tract and internal sequences.
Figure 7: Alu retrotransposition: cis and trans effects of the LINE-assisted processes.

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References

  1. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  2. Weiner, A.M., Deininger, P.L. & Efstratiadis, A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55, 631–661 (1986).

    Article  CAS  Google Scholar 

  3. Deininger, P.L. SINEs: short interspersed repeated DNA elements in higher eucaryotes. in Mobile DNA (eds. Berg, D.E. & Howe, M.M.) 619–636 (American Society for Microbiology Press, Washington, D.C., 1989).

    Google Scholar 

  4. Boeke, J.D. & Stoye, J.P. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. in Retroviruses (eds. Coffin, J.M., Hughes, S.H. & Varmus, H.E.) 343–435 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1997).

    Google Scholar 

  5. Deininger, P.L. & Batzer, M.A. Mammalian retroelements. Genome Res. 12, 1455–1465 (2002).

    Article  CAS  Google Scholar 

  6. Weiner, A.M. SINEs and LINEs: the art of biting the hand that feeds you. Curr. Opin. Cell Biol. 14, 343–350 (2002).

    Article  CAS  Google Scholar 

  7. Schmid, C.W. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26, 4541–4550 (1998).

    Article  CAS  Google Scholar 

  8. Rowold, D.J. & Herrera, R.J. Alu elements and the human genome. Genetica 108, 57–72 (2000).

    Article  CAS  Google Scholar 

  9. Batzer, M.A. & Deininger, P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3, 370–379 (2002).

    Article  CAS  Google Scholar 

  10. Weiner, A.M. An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22, 209–218 (1980).

    Article  CAS  Google Scholar 

  11. Ullu, E. & Tschudi, C. Alu sequences are processed 7SL RNA genes. Nature 312, 171–172 (1984).

    Article  CAS  Google Scholar 

  12. Quentin, Y. 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 (1992).

    Article  CAS  Google Scholar 

  13. Sinnett, D., Richer, C., Deragon, J.M. & Labuda, D. Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units. J. Biol. Chem. 266, 8675–8678 (1991).

    CAS  PubMed  Google Scholar 

  14. Bovia, F. & Strub, K. The signal recognition particle and related small cytoplasmic ribonucleoprotein particles. J. Cell. Sci. 109, 2601–2608 (1996).

    CAS  PubMed  Google Scholar 

  15. Deininger, P.L. & Batzer, M.A. Alu repeats and human disease. Mol. Genet. Metab. 67, 183–193 (1999).

    Article  CAS  Google Scholar 

  16. Kazazian, H.H.J. An estimated frequency of endogenous insertional mutations in human. Nat. Genet. 22, 130 (1999).

    Article  CAS  Google Scholar 

  17. Feng, Q., Moran, J.V., Kazazian, H.H. & Boeke, J.D. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905–916 (1996).

    Article  CAS  Google Scholar 

  18. Cost, G.J. & Boeke, J.D. Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37, 18081–18093 (1998).

    Article  CAS  Google Scholar 

  19. Cost, G.J., Feng, Q., Jacquier, A. & Boeke, J.D. Human L1 element target-primed reverse transcription in vitro. EMBO J. 21, 5899–5910 (2002).

    Article  CAS  Google Scholar 

  20. Luan, D.D., Korman, M.H., Jakubczak, J.L. & Eickbush, T.H. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72, 595–605 (1993).

    Article  CAS  Google Scholar 

  21. Jurka, J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94, 1872–1877 (1997).

    Article  CAS  Google Scholar 

  22. Esnault, C., Maestre, J. & Heidmann, T. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24, 363–367 (2000).

    Article  CAS  Google Scholar 

  23. Kajikawa, M. & Okada, N. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111, 433–444 (2002).

    Article  CAS  Google Scholar 

  24. Esnault, C., Casella, J.F. & Heidmann, T. A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells. Nucleic Acids Res. 30, e49 (2002).

    Article  Google Scholar 

  25. Sisodia, S., Sollner-Webb, B. & Cleveland, D. Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol. Cell. Biol. 7, 3602–3612 (1987).

    Article  CAS  Google Scholar 

  26. Wallace, M.R. et al. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353, 864–866 (1991).

    Article  CAS  Google Scholar 

  27. Ullu, E. & Weiner, A.M. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature 318, 371–374 (1985).

    Article  CAS  Google Scholar 

  28. Roy, A.M. et al. Upstream flanking sequences and transcription of SINEs. J. Mol. Biol. 302, 17–25 (2000).

    Article  CAS  Google Scholar 

  29. Wei, W. et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21, 1429–1439 (2001).

    Article  CAS  Google Scholar 

  30. Moran, J.V. et al. High frequency retroposition in cultured mammalian cells. Cell 87, 917–927 (1996).

    Article  CAS  Google Scholar 

  31. Jensen, S. & Heidmann, T. An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element. EMBO J. 10, 1927–1937 (1991).

    Article  CAS  Google Scholar 

  32. Moran, J.V., DeBerardinis, R.J. & Kazazian, H.H. Jr. Exon shuffling by L1 retrotransposition. Science 283, 1530–1534 (1999).

    Article  CAS  Google Scholar 

  33. Morrish, T.A. et al. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31, 159–165 (2002).

    Article  CAS  Google Scholar 

  34. Chaboissier, M.C., Finnegan, D. & Bucheton, A. Retrotransposition of the I factor, a non-long terminal repeat retrotransposon of Drosophila, generates tandem repeats at the 3′ end. Nucleic Acids Res. 28, 2467–2472 (2000).

    Article  CAS  Google Scholar 

  35. Roy-Engel, A.M. et al. Active Alu element “A-tails”: size does matter. Genome Res. 12, 1333–1344 (2002).

    Article  CAS  Google Scholar 

  36. Martin, S.L. & Bushman, F.D. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol. Cell. Biol. 21, 467–475 (2001).

    Article  CAS  Google Scholar 

  37. Kolosha, V.O. & Martin, S.L. High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1). J. Biol. Chem. 278, 8112–8117 (2003).

    Article  CAS  Google Scholar 

  38. Martin, S.L. Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol. Cell. Biol. 11, 4804–4807 (1991).

    Article  CAS  Google Scholar 

  39. Hohjoh, H. & Singer, M. Cytolasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. EMBO J. 15, 630–639 (1996).

    Article  CAS  Google Scholar 

  40. Sarrowa, J., Chang, D.Y. & Maraia, R.J. The decline in human Alu retroposition was accompanied by an asymmetric decrease in SRP9/14 binding to dimeric Alu RNA and increased expression of small cytoplasmic Alu RNA. Mol. Cell. Biol. 17, 1144–1151 (1997).

    Article  CAS  Google Scholar 

  41. Muddashetty, R. et al. Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J. Mol. Biol. 321, 433–445 (2002).

    Article  CAS  Google Scholar 

  42. West, N., Roy-Engel, A.M., Imataka, H., Sonenberg, N. & Deininger, P. Shared protein components of SINE RNPs. J. Mol. Biol. 321, 423–432 (2002).

    Article  CAS  Google Scholar 

  43. Boeke, J.D. LINEs and Alu—the poly(A) connection. Nat. Genet. 16, 6–7 (1997).

    Article  CAS  Google Scholar 

  44. Bovia, F., Fornallaz, M., Leffers, H. & Strub, K. The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs. Mol. Biol. Cell. 6, 471–484 (1995).

    Article  CAS  Google Scholar 

  45. Chang, D.Y., Sasaki-Tozawa, N., Green, L.K. & Maraia, R.J. A trinucleotide repeat-associated increase in the level of Alu RNA-binding protein occurred during the same period as the major Alu amplification that accompanied anthropoid evolution. Mol. Cell. Biol. 15, 2109–2116 (1995).

    Article  CAS  Google Scholar 

  46. Willoughby, D.A., Vilalta, A. & Oshima, R.G. An Alu element from the K18 gene confers position-independent expression in transgenic mice. J. Biol. Chem. 275, 759–768 (2000).

    Article  CAS  Google Scholar 

  47. Kimberland, M.L. et al. Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells. Hum. Mol. Genet. 8, 1557–1560 (1999).

    Article  CAS  Google Scholar 

  48. Heidmann, O. & Heidmann, T. Retrotransposition of a mouse IAP sequence tagged with an indicator gene. Cell 64, 159–170 (1991).

    Article  CAS  Google Scholar 

  49. Tchénio, T. & Heidmann, T. The dimerization/packaging sequence is dispensable for both the formation of high-molecular-weight RNA complexes within retroviral particles and the synthesis of proviruses of normal structure. J. Virol. 69, 1079–1084 (1995).

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank H. Kazazian, M. Wallace and E. Ullu for the L1-RP, Alu-NF1, and 7SL RNA gene plasmids, respectively; J. Maestre and P. Dessen for discussions; and C. Lavialle for comments and critical reading of the manuscript. This work was supported by the Centre National de la Recherche Scientifique and a grant from the Ligue Nationale Contre le Cancer (Equipe “labellisée”).

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  1. Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs, UMR 8122 CNRS, Institut Gustave Roussy, 39 rue Camille Desmoulins, Villejuif, 94805, Cedex, France

    Marie Dewannieux, Cécile Esnault & Thierry Heidmann

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Dewannieux, M., Esnault, C. & Heidmann, T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35, 41–48 (2003). https://doi.org/10.1038/ng1223

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