An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair

The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2009-03, Vol.93 (3), p.205-212
Main Authors: Srikanta, Deepa, Sen, Shurjo K., Huang, Charles T., Conlin, Erin M., Rhodes, Ryan M., Batzer, Mark A.
Format: Article
Language:English
Subjects:
Alu elements
Alu Elements - genetics
Animals
Biological and medical sciences
Computational Biology
DNA Breaks, Double-Stranded
DNA Repair
Double-strand break repair
Endonuclease-independent insertion
Fundamental and applied biological sciences. Psychology
Genes. Genome
Genetics of eukaryotes. Biological and molecular evolution
Genic rearrangement. Recombination. Transposable element
Genome, Human
Humans
Macaca mulatta
Molecular and cellular biology
Molecular genetics
Molecular Sequence Data
Pan troglodytes
Retroelements - genetics
Sequence Homology, Nucleic Acid
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Summary:The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA).
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2008.09.016