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DNA repair mediated by endonuclease-independent LINE-1 retrotransposition

Nature Genetics volume 31, pages 159–165 (2002)Cite this article

Abstract

Long interspersed elements (LINE-1s) are abundant retrotransposons in mammalian genomes that probably retrotranspose by target site-primed reverse transcription (TPRT)1,2. During TPRT, the LINE-1 endonuclease cleaves genomic DNA3, freeing a 3′ hydroxyl that serves as a primer for reverse transcription of LINE-1 RNA by LINE-1 reverse transcriptase. The nascent LINE-1 cDNA joins to genomic DNA, generating LINE-1 structural hallmarks such as frequent 5′ truncations, a 3′ poly(A)+ tail and variable-length target site duplications (TSDs)2. Here we describe a pathway for LINE-1 retrotransposition in Chinese hamster ovary (CHO) cells that acts independently of endonuclease but is dependent upon reverse transcriptase. We show that endonuclease-independent LINE-1 retrotransposition occurs at near-wildtype levels in two mutant cell lines that are deficient in nonhomologous end-joining (NHEJ). Analysis of the pre- and post-integration sites revealed that endonuclease-independent retrotransposition results in unusual structures because the LINE-1s integrate at atypical target sequences, are truncated predominantly at their 3′ ends and lack TSDs. Moreover, two of nine endonuclease-independent retrotranspositions contained cDNA fragments at their 3′ ends that are probably derived from the reverse transcription of endogenous mRNA. Thus, our results suggest that LINE-1s can integrate into DNA lesions, resulting in retrotransposon-mediated DNA repair in mammalian cells.

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Figure 1: Endonuclease-independent retrotransposition in CHO cells.
Figure 2: Structures of L1.3-derived retrotransposition events in XR-1 cells.
Figure 3: Structures of endonuclease-independent retrotransposition events.
Figure 4: A model for endonuclease-independent retrotransposition.

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References

  1. 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 

  2. Moran, J.V. & Gilbert, N. Mammalian LINE-1 retrotransposons and related elements. in Mobile DNA II (eds Craig, N., Craggie, R., Gellert, M. & Lambowitz, A.) 836–869 (ASM, Washington DC, 2002).

    Chapter  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. 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).

    Article  CAS  Google Scholar 

  6. Sassaman, D.M. et al. Many human L1 elements are capable of retrotransposition. Nature Genet. 16, 37–43 (1997).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Voliva, C.F., Martin, S.L., Hutchison, C.A.D. & Edgell, M.H. Dispersal process associated with the L1 family of interspersed repetitive DNA sequences. J. Mol. Biol. 178, 795–813 (1984).

    Article  CAS  Google Scholar 

  9. Teng, S.C., Kim, B. & Gabriel, A. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383, 641–644 (1996).

    Article  Google Scholar 

  10. Li, Z. et al. The XRCC4 gene encodes a novel protein involved in DNA double-strand break repair and V(D)J recombination. Cell 83, 1079–1089 (1995).

    Article  CAS  Google Scholar 

  11. Blunt, T. et al. Defective DNA-dependent protein kinase activity is linked to V(D)J recombination and DNA repair defects associated with the murine scid mutation. Cell 80, 813–823 (1995).

    Article  CAS  Google Scholar 

  12. Giaccia, A.J. et al. Human chromosome 5 complements the DNA double-strand break-repair deficiency and γ-ray sensitivity of the XR-1 hamster variant. Am. J. Hum. Genet. 47, 459–469 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Kojima, T., Nakajima, K. & Mikoshiba, K. The disabled 1 gene is disrupted by a replacement with L1 fragment in yotari mice. Mol. Brain Res. 75, 121–127 (2000).

    Article  CAS  Google Scholar 

  14. Mager, D., Henthorn, P. & Smithies, O. A Chinese G γ + (A γ Δ β) zero thalassemia deletion: comparison to other deletions in the human β-globin gene cluster and sequence analysis of the breakpoints. Nucleic Acids Res. 13, 6559–6575 (1985).

    Article  CAS  Google Scholar 

  15. Priestley, A. et al. Molecular and biochemical characterisation of DNA-dependent protein kinase-defective rodent mutant irs-20. Nucleic Acids Res. 26, 1965–1973 (1998).

    Article  CAS  Google Scholar 

  16. Luan, D.D. & Eickbush, T.H. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol. 15, 3882–3891 (1995).

    Article  CAS  Google Scholar 

  17. Chambeyron, S., Bucheton, A. & Busseau, I. Tandem UAA repeats at the 3′ end of the transcript are essential for precise initiation of reverse transcription of the I factor in Drosophila melanogaster. J. Biol. Chem. online publication 6 March 2002 (DOI: 10.1074/bc.M200996200).

  18. Ovchinnikov, I., Troxel, A.B. & Swergold, G.D. Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. Genome Res. 11, 2050–2058 (2001).

    Article  CAS  Google Scholar 

  19. Levin, H.L. It's prime time for reverse transcriptase. Cell 88, 5–8 (1997).

    Article  CAS  Google Scholar 

  20. Pardue, M.L., Danilevskaya, O.N., Traverse, K.L. & Lowenhaupt, K. Evolutionary links between telomeres and transposable elements. Genetica 100, 73–84 (1997).

    Article  CAS  Google Scholar 

  21. Higashiyama, T., Noutoshi, Y., Fujie, M. & Yamada, T. Zepp, a LINE-like retrotransposon accumulated in the Chlorella telomeric region. EMBO J. 16, 3715–3723 (1997).

    Article  CAS  Google Scholar 

  22. Stamato, T.D., Weinstein, R., Giaccia, A. & Mackenzie, L. Isolation of cell cycle-dependent γ ray-sensitive Chinese hamster ovary cell. Somat. Cell Genet. 9, 165–173 (1983).

    Article  CAS  Google Scholar 

  23. Fuller, L.F. & Painter, R.B. A Chinese hamster ovary cell line hypersensitive to ionizing radiation and deficient in repair replication. Mutat. Res. 193, 109–121 (1988).

    CAS  PubMed  Google Scholar 

  24. Stoneking, M. et al. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7, 1061–1071 (1997).

    Article  CAS  Google Scholar 

  25. Li, J. et al. Leukaemia disease genes: large-scale cloning and pathway predictions. Nature Genet. 23, 348–353 (1999).

    Article  CAS  Google Scholar 

  26. Carroll, M.L. et al. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311, 17–40 (2001).

    Article  CAS  Google Scholar 

  27. Dombroski, B.A., Mathias, S.L., Nanthakumar, E., Scott, A.F. & Kazazian Jr, H.H. Isolation of an active human transposable element. Science 254, 1805–1808 (1991).

    Article  CAS  Google Scholar 

  28. Narita, N. et al. Insertion of a 5′ truncated L1 element into the 3′ end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J. Clin. Invest. 91, 1862–1867 (1993).

    Article  CAS  Google Scholar 

  29. Kondo-Iida, E. et al. Novel mutations and genotype-phenotype relationships in 107 families with Fukuyama-type congenital muscular dystrophy (FCMD). Hum. Mol. Genet. 8, 2303–2309 (1999).

    Article  CAS  Google Scholar 

  30. 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 

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Acknowledgements

We thank members of the Univ. of Michigan Flow Core for help with flow cytometry, and R. Lyons at the Univ. of Michigan DNA Sequencing Core for help with sequencing. We thank T. Wilson, T. Glover, J. Goodier and current members of the Moran Lab for helpful discussions during the course of this work. J.V.M. is supported in part by grants from the W.M. Keck Foundation and the National Institutes of Health (NIH). M.A.B. is supported in part by the NIH and the Louisiana Board of Regents Millennium Trust Health Excellence Fund. G.E.T is a scholar of the Leukemia and Lymphoma Society and receives lab support from the NIH and the Aids for Cancer Research. T.D.S. is supported by grants from the NIH. T.A.M. was supported in part by an NIH training grant. Sequencing costs were defrayed partly by a grant to the Univ. of Michigan Cancer Center.

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Authors and Affiliations

  1. Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, 48105-0618, Michigan, USA

    Tammy A. Morrish, Nicolas Gilbert & John V. Moran

  2. Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, USA

    Jeremy S. Myers, Bethaney J. Vincent & Mark A. Batzer

  3. Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, USA

    Thomas D. Stamato

  4. Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA

    Guillermo E. Taccioli

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Correspondence to John V. Moran.

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Morrish, T., Gilbert, N., Myers, J. et al. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 31, 159–165 (2002). https://doi.org/10.1038/ng898

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