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Proc Natl Acad Sci U S A. 2014 May 6;111(18):6684-9. doi: 10.1073/pnas.1321854111. Epub 2014 Apr 23.

Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair.

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  • 1Department of Genetics, University of Georgia, Athens, GA 30602.

Abstract

The insertion of DNA into a genome can result in the duplication and dispersal of functional sequences through the genome. In addition, a deeper understanding of insertion mechanisms will inform methods of genetic engineering and plant transformation. Exploiting structural variations in numerous rice accessions, we have inferred and analyzed intermediate length (10-1,000 bp) insertions in plants. Insertions in this size class were found to be approximately equal in frequency to deletions, and compound insertion-deletions comprised only 0.1% of all events. Our findings indicate that, as observed in humans, tandem or partially tandem duplications are the dominant form of insertion (48%), although short duplications from ectopic donors account for a sizable fraction of insertions in rice (38%). Many nontandem duplications contain insertions from nearby DNA (within 200 bp) and can contain multiple donor sources--some distant--in single events. Although replication slippage is a plausible explanation for tandem duplications, the end homology required in such a model is most often absent and rarely is >5 bp. However, end homology is commonly longer than expected by chance. Such findings lead us to favor a model of patch-mediated double-strand-break creation followed by nonhomologous end-joining. Additionally, a striking bias toward 31-bp partially tandem duplications suggests that errors in nucleotide excision repair may be resolved via a similar, but distinct, pathway. In summary, the analysis of recent insertions in rice suggests multiple underappreciated causes of structural variation in eukaryotes.

KEYWORDS:

double-strand break repair; structural DNA variation

PMID:
24760826
[PubMed - indexed for MEDLINE]
PMCID:
PMC4020087
Free PMC Article
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