Elsevier

Genomics

Volume 93, Issue 3, March 2009, Pages 205-212
Genomics

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

https://doi.org/10.1016/j.ygeno.2008.09.016Get rights and content
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Abstract

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).

Abbreviations

NCAI
non-classical Alu insertion
CS
chimpanzee-specific
HS
human-specific
RS
rhesus-specific
DSBs
double-strand breaks
TPRT
target-site primed reverse transcription
SDSA
synthesis dependent strand annealing
IVRR
in vitro RNA recombination
PCR
polymerase chain reaction
NHEJ
non-homologous end-joining
EN
endonuclease
RT
reverse transcriptase
SINE
short interspersed element
OWM
Old World monkey
RM
RepeatMasker
TSD
target site duplication

Keywords

Alu elements
Endonuclease-independent insertion
Double-strand break repair

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