Internal priming: An opportunistic pathway for L1 and Alu retrotransposition in hominins
- 15 December 2009
- journal article
- Published by Elsevier BV in Gene
- Vol. 448 (2), 233-241
- https://doi.org/10.1016/j.gene.2009.05.014
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′ poly-A 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.Keywords
This publication has 46 references indexed in Scilit:
- An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repairGenomics, 2009
- Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?Genome Research, 2009
- The diversity of retrotransposons and the properties of their reverse transcriptasesVirus Research, 2008
- Alternative endingsProceedings of the National Academy of Sciences of the United States of America, 2008
- DNA-directed DNA Polymerase and Strand Displacement Activity of the Reverse Transcriptase Encoded by the R2 RetrotransposonJournal of Molecular Biology, 2007
- Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genomeNucleic Acids Research, 2007
- Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrityMutation Research, 2006
- Alu repeats and human genomic diversityNature Reviews Genetics, 2002
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- The impact of L1 retrotransposons on the human genomeNature Genetics, 1998