Rescuing Alu

Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

Bradley J. Wagstaff, Dale J. Hedges, Rebecca S. Derbes, Rebeca Campos Sanchez, Francesca Chiaromonte, Kateryna Dmytrivna Makova, Astrid M. Roy-Engel

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Alu elements are trans-mobilized by the autonomous non-LTR retroelement, LINE-1 (L1). Alu-induced insertion mutagenesis contributes to about 0.1% human genetic disease and is responsible for the majority of the documented instances of human retroelement insertion-induced disease. Here we introduce a SINE recovery method that provides a complementary approach for comprehensive analysis of the impact and biological mechanisms of Alu retrotransposition. Using this approach, we recovered 226 de novo tagged Alu inserts in HeLa cells. Our analysis reveals that in human cells marked Alu inserts driven by either exogenously supplied full length L1 or ORF2 protein are indistinguishable. Four percent of de novo Alu inserts were associated with genomic deletions and rearrangements and lacked the hallmarks of retrotransposition. In contrast to L1 inserts, 5′ truncations of Alu inserts are rare, as most of the recovered inserts (96.5%) are full length. De novo Alus show a random pattern of insertion across chromosomes, but further characterization revealed an Alu insertion bias exists favoring insertion near other SINEs, highly conserved elements, with almost 60% landing within genes. De novo Alu inserts show no evidence of RNA editing. Priming for reverse transcription rarely occurred within the first 20 bp (most 5′) of the A-tail. The A-tails of recovered inserts show significant expansion, with many at least doubling in length. Sequence manipulation of the construct led to the demonstration that the A-tail expansion likely occurs during insertion due to slippage by the L1 ORF2 protein. We postulate that the A-tail expansion directly impacts Alu evolution by reintroducing new active source elements to counteract the natural loss of active Alus and minimizing Alu extinction.

Original languageEnglish (US)
Article numbere1002842
JournalPLoS genetics
Volume8
Issue number8
DOIs
StatePublished - Aug 1 2012

Fingerprint

preserves
Tail
tail
Short Interspersed Nucleotide Elements
Retroelements
recovery method
protein
retrotransposons
RNA
chromosome
genomics
extinction
Alu Elements
RNA Editing
RNA editing
Inborn Genetic Diseases
reverse transcription
gene
Medical Genetics
genetic disorders

All Science Journal Classification (ASJC) codes

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Wagstaff, Bradley J. ; Hedges, Dale J. ; Derbes, Rebecca S. ; Campos Sanchez, Rebeca ; Chiaromonte, Francesca ; Makova, Kateryna Dmytrivna ; Roy-Engel, Astrid M. / Rescuing Alu : Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion. In: PLoS genetics. 2012 ; Vol. 8, No. 8.
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abstract = "Alu elements are trans-mobilized by the autonomous non-LTR retroelement, LINE-1 (L1). Alu-induced insertion mutagenesis contributes to about 0.1{\%} human genetic disease and is responsible for the majority of the documented instances of human retroelement insertion-induced disease. Here we introduce a SINE recovery method that provides a complementary approach for comprehensive analysis of the impact and biological mechanisms of Alu retrotransposition. Using this approach, we recovered 226 de novo tagged Alu inserts in HeLa cells. Our analysis reveals that in human cells marked Alu inserts driven by either exogenously supplied full length L1 or ORF2 protein are indistinguishable. Four percent of de novo Alu inserts were associated with genomic deletions and rearrangements and lacked the hallmarks of retrotransposition. In contrast to L1 inserts, 5′ truncations of Alu inserts are rare, as most of the recovered inserts (96.5{\%}) are full length. De novo Alus show a random pattern of insertion across chromosomes, but further characterization revealed an Alu insertion bias exists favoring insertion near other SINEs, highly conserved elements, with almost 60{\%} landing within genes. De novo Alu inserts show no evidence of RNA editing. Priming for reverse transcription rarely occurred within the first 20 bp (most 5′) of the A-tail. The A-tails of recovered inserts show significant expansion, with many at least doubling in length. Sequence manipulation of the construct led to the demonstration that the A-tail expansion likely occurs during insertion due to slippage by the L1 ORF2 protein. We postulate that the A-tail expansion directly impacts Alu evolution by reintroducing new active source elements to counteract the natural loss of active Alus and minimizing Alu extinction.",
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Rescuing Alu : Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion. / Wagstaff, Bradley J.; Hedges, Dale J.; Derbes, Rebecca S.; Campos Sanchez, Rebeca; Chiaromonte, Francesca; Makova, Kateryna Dmytrivna; Roy-Engel, Astrid M.

In: PLoS genetics, Vol. 8, No. 8, e1002842, 01.08.2012.

Research output: Contribution to journalArticle

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AU - Wagstaff, Bradley J.

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