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RNA-templated DNA repair

An Erratum to this article was published on 30 August 2007

Abstract

RNA can act as a template for DNA synthesis in the reverse transcription of retroviruses and retrotransposons1 and in the elongation of telomeres2. Despite its abundance in the nucleus, there has been no evidence for a direct role of RNA as a template in the repair of any chromosomal DNA lesions, including DNA double-strand breaks (DSBs), which are repaired in most organisms by homologous recombination or by non-homologous end joining3. An indirect role for RNA in DNA repair, following reverse transcription and formation of a complementary DNA, has been observed in the non-homologous joining of DSB ends4,5. In the yeast Saccharomyces cerevisiae, in which homologous recombination is efficient3, RNA was shown to mediate recombination, but only indirectly through a cDNA intermediate6,7 generated by the reverse transcriptase function of Ty retrotransposons in Ty particles in the cytoplasm8. Although pairing between duplex DNA and single-strand (ss)RNA can occur in vitro9,10 and in vivo11, direct homologous exchange of genetic information between RNA and DNA molecules has not been observed. We show here that RNA can serve as a template for DNA synthesis during repair of a chromosomal DSB in yeast. The repair was accomplished with RNA oligonucleotides complementary to the broken ends. This and the observation that even yeast replicative DNA polymerases such as α and δ can copy short RNA template tracts in vitro demonstrate that RNA can transfer genetic information in vivo through direct homologous interaction with chromosomal DNA.

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Figure 1: Repair of a DSB by RNA-containing oligonucleotides.
Figure 2: Strand bias of oligonucleotide targeting to sites distant from the DSB.
Figure 3: Synthesis by Pol α and Pol δ across RNA templates.

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Acknowledgements

We thank J. E. Haber for yeast strain YFP17 and P. M. J. Burgers for yeast DNA polymerase δ. We thank C. Halweg and W. C. Copeland for suggestions; K. L. Adelman, J. W. Drake and A. Sugino for critical reading of the manuscript; and J. R. Snipe and G. K. Chan for technical assistance. Research support was from National Institute of Environmental Health Sciences (NIH) intramural research funds.

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Correspondence to Michael A. Resnick.

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Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-5, Supplementary Notes, Supplementary Methods and Supplementary Figure 1. Supplementary Table 1 provides the sequence information of all the oligonucleotides used in this work. Supplementary Tables 2-5 present the complete data set and statistical analysis of transformation frequencies obtained with the different oligonucleotides in wild-type cells and in several mutant backgrounds. Supplementary Notes contain additional reference #30 cited in Supplementary Table 5 legend. Supplementary Methods contain details about yeast strains and details about DSB induction. Supplementary Figure 1 presents a control experiment where the oligonucleotides have been treated with alkali. The data show that targeting events obtained with RNA-containing oligonucleotides are not due to contamination with DNA molecules. (PDF 1072 kb)

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Storici, F., Bebenek, K., Kunkel, T. et al. RNA-templated DNA repair. Nature 447, 338–341 (2007). https://doi.org/10.1038/nature05720

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