Genetic Evidence That the Non-Homologous End-Joining Repair Pathway Is Involved in LINE Retrotransposition

Jun Suzuki,Kenji Ichiyanagi,Norihiro Okada,Masaki Kajikawa,Shunichi Takeda,Katsumi Yamaguchi,Noritaka Adachi,Hideki Koyama,Harmit S Malik

doi:10.1371/journal.pgen.1000461

Abstract

Long interspersed elements (LINEs) are transposable elements that proliferate within eukaryotic genomes, having a large impact on eukaryotic genome evolution. LINEs mobilize via a process called retrotransposition. Although the role of the LINE-encoded protein(s) in retrotransposition has been extensively investigated, the participation of host-encoded factors in retrotransposition remains unclear. To address this issue, we examined retrotransposition frequencies of two structurally different LINEs—zebrafish ZfL2-2 and human L1—in knockout chicken DT40 cell lines deficient in genes involved in the non-homologous end-joining (NHEJ) repair of DNA and in human HeLa cells treated with a drug that inhibits NHEJ. Deficiencies of NHEJ proteins decreased retrotransposition frequencies of both LINEs in these cells, suggesting that NHEJ is involved in LINE retrotransposition. More precise characterization of ZfL2-2 insertions in DT40 cells permitted us to consider the possibility of dual roles for NHEJ in LINE retrotransposition, namely to ensure efficient integration of LINEs and to restrict their full-length formation.

Highlights

Long interspersed elements (LINEs) and short interspersed elements (SINEs) are transposable elements widely distributed in eukaryotic genomes [1,2]; as such, they substantially affect genome complexity and evolution [3,4]
LINEs had been considered as ‘‘junk’’ DNA, recent studies have suggested that the LINE-induced alterations of host chromosomes are a major driving force for eukaryotic genome evolution
LINEs mobilize via a mechanism called retrotransposition, in which transcribed LINE RNA is reverse transcribed into DNA that is integrated into the host chromosome

Summary

Introduction

Long interspersed elements (LINEs) and short interspersed elements (SINEs) are transposable elements widely distributed in eukaryotic genomes [1,2]; as such, they substantially affect genome complexity and evolution [3,4] These elements mobilize and amplify their own sequences by a mechanism called retrotransposition. The LINE mRNA and proteins form a complex [7,8] and move to target sites on a host chromosome where the LINEencoded endonuclease (EN) nicks a strand on the DNA duplex. It is conceivable that the LINE retrotransposition reactions involve other host factors, such as proteins of the non-homologous end-joining (NHEJ) pathway, that predominate in DSB repair in vertebrate cells [15]

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Discussion

Conclusion