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

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.

Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells

“…These data are consistent with the hypothesis that the resultant L1 retrotransposition insertions are longer in ATM-deficient NPCs compared with ATM-proficient controls. Notably, a similar finding indicated that deficiencies in NHEJ resulted in longer insertions when assaying a zebrafish LINE element in chicken DT40 cells (15). Thus, we speculate that ATM may recognize intermediates that are generated during the process of L1 integration as DNA damage and thereby reduce the length of the resultant retrotransposition events (Fig.…”

“…Notably, most genomic L1 insertions are 5′ truncated (1,38). Because the L1 ORF2p RT has been shown to be highly processive in vitro (39), we hypothesized that cellular DNA repair and damage sensing proteins may impact L1 5′ truncation (15,17). If so, the loss of ATM may lead to longer, or perhaps more, L1 insertions in ATM-deficient cells.…”

“…For example, DNA repair pathways may either inhibit L1 retrotransposition or lead to L1 5′ truncation of de novo insertions (14,15). Studies of cultured cells and comparative genomics analyses have further demonstrated that L1 retrotransposition events are associated with various genomic structural DNA rearrangements, which include intrachromosomal deletions, intrachromosomal duplication/inversions, and perhaps interchromosomal translocations (11,(16)(17)(18)(19)(20).…”

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

“…Also like group II intron RTs (72,73), mammalian LINE-1 elements and most other non-LTR-retrotransposon RTs lack an RNase H domain and may rely at least in part on a host RNase H for degradation of the RNA template strand in addition to strand displacement by the RT (136,151). Additionally, the TPRT mechanism used by non-LTR-retrotransposons results in a cDNA whose 3′ end may be ligated to upstream sequences by NHEJ enzymes (152), analogous to the retrohoming mechanism used by linear group II introns (see above), or linked to upstream sequences via template switching, a proficient activity of both group II intron and non-LTR-retrotransposon RTs (68,136,153,154). Finally, the mechanism used for second-strand DNA synthesis by non-LTR-retrotransposons is not known, but given their nuclear localization could involve a host DNA polymerase, similar to mobile group II introns (73), rather than the DNA-dependent polymerase activity of the RT.…”

Rétrotransposons et cellules somatiques

“…Ce mécanisme est nommé target-primed reverse transcriptase (TPRT) ( Figure 1B). Cependant, les copies de L1 nouvellement intégrées sont souvent tronquées en 5' ; ceci ne serait pas dû à la faible activité RT de l'ORF2p [7], mais plus vraisemblablement à des facteurs protéiques associés aux mécanismes de réparation de l'ADN [8][9][10]. La détection des transcrits de L1 et de la protéine ORF2p s'avère difficile dans les cellules de mammifères, même dans le contexte d'expériences de surexpression, suggérant qu'un mécanisme spécifique régule l'expression des L1 dans …”