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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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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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