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.

Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells


Long interspersed element-1 (LINE-1 or L1) retrotransposition continues to affect human genome evolution1,2. L1s can retrotranspose in the germline, during early development and in select somatic cells3,4,5,6,7,8; however, the host response to L1 retrotransposition remains largely unexplored. Here we show that reporter genes introduced into the genome of various human embryonic carcinoma-derived cell lines (ECs) by L1 retrotransposition are rapidly and efficiently silenced either during or immediately after their integration. Treating ECs with histone deacetylase inhibitors rapidly reverses this silencing, and chromatin immunoprecipitation experiments revealed that reactivation of the reporter gene was correlated with changes in chromatin status at the L1 integration site. Under our assay conditions, rapid silencing was also observed when reporter genes were delivered into ECs by mouse L1s and a zebrafish LINE-2 element, but not when similar reporter genes were delivered into ECs by Moloney murine leukaemia virus or human immunodeficiency virus, suggesting that these integration events are silenced by distinct mechanisms. Finally, we demonstrate that subjecting ECs to culture conditions that promote differentiation attenuates the silencing of reporter genes delivered by L1 retrotransposition, but that differentiation, in itself, is not sufficient to reactivate previously silenced reporter genes. Thus, our data indicate that ECs differ from many differentiated cells in their ability to silence reporter genes delivered by L1 retrotransposition.

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: L1 expression and retrotransposition in EC cells.
Figure 2: Engineered L1 retrotransposition events are efficiently silenced in EC cells.
Figure 3: Analyses of L1 silencing in a clonal (pk-5) cell line.
Figure 4: Analysis of L1 silencing in differentiating cells.


  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. Goodier, J. L. & Kazazian, H. H. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135, 23–35 (2008)

    CAS  Article  Google Scholar 

  3. Garcia-Perez, J. L. et al. LINE-1 retrotransposition in human embryonic stem cells. Hum. Mol. Genet. 16, 1569–1577 (2007)

    CAS  Article  Google Scholar 

  4. Kano, H. et al. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev. 23, 1303–1312 (2009)

    CAS  Article  Google Scholar 

  5. Muotri, A. R. et al. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435, 903–910 (2005)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  7. van den Hurk, J. A. et al. L1 retrotransposition can occur early in human embryonic development. Hum. Mol. Genet. 16, 1587–1592 (2007)

    CAS  Article  Google Scholar 

  8. Coufal, N. G. et al. L1 retrotransposition in human neural progenitor cells. Nature 460, 1127–1131 (2009)

    ADS  CAS  Article  Google Scholar 

  9. Sperger, J. M. et al. Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc. Natl Acad. Sci. USA 100, 13350–13355 (2003)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  11. Brouha, B. et al. Evidence consistent with human L1 retrotransposition in maternal meiosis I. Am. J. Hum. Genet. 71, 327–336 (2002)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  14. Ostertag, E. M., Prak, E. T., DeBerardinis, R. J., Moran, J. V. & Kazazian, H. H., Jr Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res. 28, 1418–1423 (2000)

    CAS  Article  Google Scholar 

  15. Goodier, J. L., Ostertag, E. M., Du, K. & Kazazian, H. H., Jr A novel active L1 retrotransposon subfamily in the mouse. Genome Res. 11, 1677–1685 (2001)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  17. Sugano, T., Kajikawa, M. & Okada, N. Isolation and characterization of retrotransposition-competent LINEs from zebrafish. Gene 365, 74–82 (2006)

    CAS  Article  Google Scholar 

  18. Loh, T. P., Sievert, L. L. & Scott, R. W. Proviral sequences that restrict retroviral expression in mouse embryonal carcinoma cells. Mol. Cell. Biol. 7, 3775–3784 (1987)

    CAS  Article  Google Scholar 

  19. Teich, N. M., Weiss, R. A., Martin, G. R. & Lowy, D. R. Virus infection of murine teratocarcinoma stem cell lines. Cell 12, 973–982 (1977)

    CAS  Article  Google Scholar 

  20. Wolf, D. & Goff, S. P. TRIM28 mediates primer binding site-targeted silencing of murine leukemia virus in embryonic cells. Cell 131, 46–57 (2007)

    CAS  Article  Google Scholar 

  21. Wolf, D. & Goff, S. P. Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 458, 1201–1204 (2009)

    ADS  CAS  Article  Google Scholar 

  22. Li, X. et al. Generation of destabilized green fluorescent protein as a transcription reporter. J. Biol. Chem. 273, 34970–34975 (1998)

    CAS  Article  Google Scholar 

  23. Gummow, B. M., Scheys, J. O., Cancelli, V. R. & Hammer, G. D. Reciprocal regulation of a glucocorticoid receptor-steroidogenic factor-1 transcription complex on the Dax-1 promoter by glucocorticoids and adrenocorticotropic hormone in the adrenal cortex. Mol. Endocrinol. 20, 2711–2723 (2006)

    CAS  Article  Google Scholar 

  24. Matthaei, K. I., Andrews, P. W. & Bronson, D. L. Retinoic acid fails to induce differentiation in human teratocarcinoma cell lines that express high levels of a cellular receptor protein. Exp. Cell Res. 143, 471–474 (1983)

    CAS  Article  Google Scholar 

  25. Kubo, S. et al. L1 retrotransposition in nondividing and primary human somatic cells. Proc. Natl Acad. Sci. USA 103, 8036–8041 (2006)

    ADS  CAS  Article  Google Scholar 

  26. Bestor, T. H. & Tycko, B. Creation of genomic methylation patterns. Nature Genet. 12, 363–367 (1996)

    CAS  Article  Google Scholar 

  27. Bourc'his, D. & Bestor, T. H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99 (2004)

    ADS  CAS  Article  Google Scholar 

  28. Schumann, G. G. APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition. Biochem. Soc. Trans. 35, 637–642 (2007)

    CAS  Article  Google Scholar 

  29. Stetson, D. B., Ko, J. S., Heidmann, T. & Medzhitov, R. Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell 134, 587–598 (2008)

    CAS  Article  Google Scholar 

  30. Suzuki, J. et al. Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet. 5, e1000461 (2009)

    Article  Google Scholar 

Download references


We thank P. W. Andrews for providing human EC lines, discussing unpublished data from his laboratory and giving advice during the course of this study. We thank A. Macia and M. Munoz-Lopez (Andalusian Stem Cell Bank) for sharing unpublished data; A. V. Furano, H. Kazazian, J. K. Kim, H. Kopera, A. Muotri, and members of the Moran and Garcia-Perez laboratories for critical reading of the manuscript; and G. Smith and L. Villa for help in creating the time-lapsed movie. We thank M. Velkey for providing plasmid pBSSK-pgk; H. Kazazian for providing plasmid pJCC5/LRE3; J. Boeke for providing synthetic mouse LINE-1 constructs; M. Kajikawa and N. Okada for providing the zebrafish LINE-2 expression plasmids; T. Fanning for providing the polyclonal ORF1 antibody; I. Damjanov for comments on the teratoma characterization; T. Lanigan for preparing Moloney murine leukaemia virus retroviral supernatants; C. Pigott for EC culture advice; and T. de la Cueva, P. Catalina and A. Nieto (Andalusian Stem Cell Bank) for their help with mouse experimentation, SKY-FISH and pathology analyses, respectively. J.V.M. is supported by the National Institutes of Health (NIH) (GM060518 and GM082970) and the Howard Hughes Medical Institute. J.L.G.-P. is supported by the Instituto de Salud Carlos III - Consejeria de Salud Junta de Andalucia (ISCIII-CSJA) (EMER07/056), by a Marie Curie International Reintegration Grant action (FP7-PEOPLE-2007-4-3-IRG), by CICE (P09-CTS-4980) and Proyectos en Salud (PI0002/2009) from Junta de Andalucia (Spain) and through the Spanish Ministry of Health (FIS PI08171 and Miguel Servet CP07/00065). M.M. is supported by the ISCIII-CSJA (EMER07/056). P.M. is supported by the Spanish Ministry of Science and Innovation MICINN-PLANE (PLE-2009-0111), by CICE (P08-CTS-3678) from Junta de Andalucia (Spain) and by the Spanish Ministry of Health (FIS PI070026). K.S.O’S. is supported by the NIH (NS-048187 and GM-069985). K.L.C. is supported by the Burroughs Wellcome Foundation and by an NIH Research Project Grant (R01) (AI051198). G.D.H is supported by a National Institute of Diabetes and Digestive and Kidney Diseases NIH R01 (DK62027). J.O.S. is supported by a Cellular and Molecular Approaches to Systems and Integrative Biology Training Grant (T32-GM08322). D.A.K. is supported by The Irvington Institute Fellowship Program of the Cancer Research Institute. S.M. is supported by a CICE (P08-CTS-3678) scholarship from Junta de Andalucia, Spain. C.C.C. is supported by a Rackham Predoctoral Fellowship from the University of Michigan. We defrayed the costs of DNA sequencing in part with the University of Michigan's Cancer Center Support Grant (NIH 5 P30 CA46592).

Author information

Authors and Affiliations



J.V.M. and J.L.G.-P. directed the project, designed experiments and drafted the manuscript. J.L.G.-P. performed experiments with the assistance of M.M. and K.S.O’S. (cell cycle experiments), J.O.S. and G.D.H (chromatin immunoprecipitation experiments), D.A.K., C.C.C. and K.L.C. (human immunodeficiency virus-based experiments), and S.M. and P.M. (teratoma assays). All the authors commented on the manuscript.

Corresponding authors

Correspondence to Jose L. Garcia-Perez or John V. Moran.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, legend for Supplementary Movie 1, Supplementary Tables 1-2, Supplementary Figures 1-10 with legends and References. (PDF 17434 kb)

Supplementary Movie 1

This movie shows reactivation of L1-retro-EGFP expression in pk-5 Cells (see page 17 of the Supplementary Information file for full legend). (MOV 962 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Garcia-Perez, J., Morell, M., Scheys, J. et al. Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466, 769–773 (2010).

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