Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A highly active synthetic mammalian retrotransposon


LINE-1 (L1) elements are retrotransposons that comprise large fractions of mammalian genomes1. Transcription through L1 open reading frames is inefficient owing to an elongation defect2, inhibiting the robust expression of L1 RNA and proteins, the substrate and enzyme(s) for retrotransposition3,4,5. This elongation defect probably controls L1 transposition frequency in mammalian cells. Here we report bypassing this transcriptional defect by synthesizing the open reading frames of L1 from synthetic oligonucleotides, altering 24% of the nucleic acid sequence without changing the amino acid sequence. Such resynthesis led to greatly enhanced steady-state L1 RNA and protein levels. Remarkably, when the synthetic open reading frames were substituted for the wild-type open reading frames in an established retrotransposition assay4, transposition levels increased more than 200-fold. This indicates that there are probably no large, rigidly conserved cis-acting nucleic acid sequences required for retrotransposition within L1 coding regions. These synthetic retrotransposons are also the most highly active L1 elements known so far and have potential as practical tools for manipulating mammalian genomes.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Synthesis and expression of synthetic mouse ORF2.
Figure 2: Retrotransposition of synthetic mL1.
Figure 3: Synthetic mouse L1 uses the standard retrotransposition mechanism.
Figure 4: High-frequency retrotransposition in mouse cells: total RNA analysis of smL1 expression.


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

    ADS  CAS  Article  Google Scholar 

  2. Han, J. S., Szak, S. T. & Boeke, J. D. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429, 268–274 (2004)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  5. 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)

    CAS  Article  Google Scholar 

  6. Dewannieux, M., Esnault, C. & Heidmann, T. LINE-mediated retrotransposition of marked Alu sequences. Nature Genet. 35, 41–48 (2003)

    CAS  Article  Google Scholar 

  7. Martin, S. L. Characterization of a LINE-1 cDNA that originated from RNA present in the ribonucleoprotein particles: implications for the structure of an active mouse LINE-1. Gene 153, 261–266 (1995)

    CAS  Article  Google Scholar 

  8. Kolosha, V. O. & Martin, S. L. In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Proc. Natl Acad. Sci. USA 94, 10155–10160 (1997)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  11. Mathias, S. L., Scott, A. F., Kazazian, H. H. Jr, Boeke, J. D. & Gabriel, A. Reverse transcriptase encoded by a human transposable element. Science 254, 1808–1810 (1991)

    ADS  CAS  Article  Google Scholar 

  12. Stemmer, W. P., Crameri, A., Ha, K. D., Brennan, T. M. & Heyneker, H. L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49–53 (1995)

    CAS  Article  Google Scholar 

  13. Boissinot, S., Chevret, P. & Furano, A. V. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17, 915–928 (2000)

    CAS  Article  Google Scholar 

  14. Gilbert, N., Lutz-Prigge, S. & Moran, J. V. Genomic deletions created upon LINE-1 retrotransposition. Cell 110, 315–325 (2002)

    CAS  Article  Google Scholar 

  15. Symer, D. E. et al. Human L1 retrotransposition is associated with genetic instability in vivo. Cell 110, 327–338 (2002)

    CAS  Article  Google Scholar 

  16. 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)

    CAS  Article  Google Scholar 

  17. Wei, W., Morrish, T. A., Alisch, R. S. & Moran, J. V. A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Anal. Biochem. 284, 435–438 (2000)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  19. Hamer, L., DeZwaan, T. M., Montenegro-Chamorro, M. V., Frank, S. A. & Hamer, J. E. Recent advances in large-scale transposon mutagenesis. Curr. Opin. Chem. Biol. 5, 67–72 (2001)

    CAS  Article  Google Scholar 

  20. Ostertag, E. M. et al. A mouse model of human L1 retrotransposition. Nature Genet. 32, 655–660 (2002)

    CAS  Article  Google Scholar 

  21. Haas, J., Park, E.-C. & Seed, B. Codon usage limitation in the expression of HIV-1 envelope glycoprotein. Curr. Biol. 6, 315–324 (1996)

    CAS  Article  Google Scholar 

  22. Naas, T. P. et al. An actively retrotransposing, novel subfamily of mouse L1 elements. EMBO J. 17, 590–597 (1998)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

Download references


We thank Boeke laboratory members, especially Y. Aizawa, for helpful discussions and critical reading of the manuscript. We thank A. Yetil for assistance. This work was supported by the NIH (J.D.B.) and the Medical Scientist Training Program (J.S.H.).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Jef D. Boeke.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Legends

Legends for Supplementary Tables S1, S2 and Supplementary Figure S1 (DOC 30 kb)

Supplementary Tables

Supplementary Table S1:Oligonucleotides used; Supplementary Table S2: Codons used to synthesize smORF1 and smORF2. (PDF 17 kb)

Supplementary Figure S1

Alignment of native mouse L1 with synthetic mouse L1. (PDF 123 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Han, J., Boeke, J. A highly active synthetic mammalian retrotransposon. Nature 429, 314–318 (2004).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing