Internal priming: An opportunistic pathway for L1 and Alu retrotransposition in hominins

Abstract

Retrotransposons, specifically Alu and L1 elements, have been especially successful in their expansion throughout primate genomes. While most of these elements integrate through an endonuclease-mediated process termed target primed reverse transcription, a minority integrate using alternative methods. Here we present evidence for one such mechanism, (which we term internal priming) and demonstrate that loci integrating through this mechanism are qualitatively different from “classical” insertions. Previous examples of this mechanism are limited to cell culture assays, which show that reverse transcription can initiate upstream of the 3′ polyA tail during retrotransposon integration. To detect whether this mechanism occurs in vivo as well as in cell culture, we have analyzed the human genome for internal priming events using recently integrated L1 and Alu elements. Our examination of the human genome resulted in the recovery of twenty events involving internal priming insertions, which are structurally distinct from both classical TPRT-mediated insertions and non-classical insertions. We suggest two possible mechanisms by which these internal priming loci are created and provide evidence supporting a role in staggered DNA double-strand break repair. Also, we demonstrate that the internal priming process is associated with inter-chromosomal duplications and the insertion of filler DNA.

Active human retrotransposons: variation and disease

“…Another example (Table 2, [61]) indicates internal priming by L1 RT [49,62] occurred at an internal L1 RNA A-rich stretch, resulting in a 3’-truncated L1 insertion [63] in the EYA1 gene [61]. Furthermore, it became clear while annotating the TSDs and L1 EN cleavage sites (consensus bottom strand 5’-YYYY/RR-3’, where Y represents pyrimidine and R represents purine) for the disease-causing insertions that there were a subset of 5 that had poor EN cleavage sites (YYYY/YN).…”

Pathogenesis of Chagas' Disease: Parasite Persistence and Autoimmunity

“…The mobilization of retroelements requires DNA doublestrand-break (DSB) repair (261,377,384,467). A DSB is a genotoxic lesion that can be caused by a microorganism's invasion.…”

LINEs, SINEs and other retroelements: do birds of a feather flock together?

“…Although very inefficiently, the retrotransposition of Alu transcripts without 3’ poly-A stretches can occur (83). In addition, the presence of a few “tailless” 3’ truncated Alu inserts in the human genome indicates the likely occurrence of internal priming during the TPRT step (90) (Figure 4). Also, a large number of retrotransposed copies of RNA pol III transcripts (tRNA, tRNA-related, and 4.5S RNA) that lack A-tails and referred to as tailless retropseudogenes have been described (29).…”