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

Genomics. 2009 Mar;93(3):205-12. doi: 10.1016/j.ygeno.2008.09.016. Epub 2008 Nov 11.


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).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alu Elements / genetics*
  • Animals
  • Computational Biology
  • DNA Breaks, Double-Stranded*
  • DNA Repair*
  • Genome, Human
  • Humans
  • Macaca mulatta
  • Molecular Sequence Data
  • Pan troglodytes
  • Retroelements / genetics*
  • Sequence Homology, Nucleic Acid


  • Retroelements

Associated data

  • GENBANK/EU263070
  • GENBANK/EU263071
  • GENBANK/EU263072
  • GENBANK/EU263073
  • GENBANK/EU263074
  • GENBANK/EU263075
  • GENBANK/EU263076
  • GENBANK/EU263077
  • GENBANK/EU263078
  • GENBANK/EU263079
  • GENBANK/EU263080
  • GENBANK/EU263081
  • GENBANK/EU263082
  • GENBANK/EU263083
  • GENBANK/EU263084
  • GENBANK/EU263085
  • GENBANK/EU263086
  • GENBANK/EU263087
  • GENBANK/EU263088
  • GENBANK/EU263089
  • GENBANK/EU263090
  • GENBANK/EU263091
  • GENBANK/EU263092
  • GENBANK/EU263093
  • GENBANK/EU263094
  • GENBANK/EU263095
  • GENBANK/EU263096
  • GENBANK/EU263097
  • GENBANK/EU263098
  • GENBANK/EU263099
  • GENBANK/EU263100
  • GENBANK/EU263101
  • GENBANK/EU263102