DNA repair mediated by endonuclease-independent LINE-1 retrotransposition

Tammy A. Morrish, University of Michigan Medical School
Nicolas Gilbert, University of Michigan Medical School
Jeremy S. Myers, Louisiana State University
Bethaney J. Vincent, Louisiana State University
Thomas D. Stamato, Lankenau Institute for Medical Research
Guillermo E. Taccioli, Boston University School of Medicine
Mark A. Batzer, Louisiana State University
John V. Moran, University of Michigan Medical School

Abstract

Long interspersed elements (LINE-1s) are abundant retro-transposons in mammalian genomes that probably retro-transpose by target site-primed reverse transcription (TPRT). During TPRT, the LINE-1 endonuclease cleaves genomic DNA, 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). 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.