Brief Communication | Published:

Accurate identification of human Alu and non-Alu RNA editing sites

Nature Methods volume 9, pages 579581 (2012) | Download Citation

Abstract

We developed a computational framework to robustly identify RNA editing sites using transcriptome and genome deep-sequencing data from the same individual. As compared with previous methods, our approach identified a large number of Alu and non-Alu RNA editing sites with high specificity. We also found that editing of non-Alu sites appears to be dependent on nearby edited Alu sites, possibly through the locally formed double-stranded RNA structure.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    , , , & Nat. Struct. Mol. Biol. 18, 230–236 (2011).

  2. 2.

    Annu. Rev. Biochem. 79, 321–349 (2010).

  3. 3.

    et al. Nat. Biotechnol. 22, 1001–1005 (2004).

  4. 4.

    & Curr. Opin. Genet. Dev. 21, 401–406 (2011).

  5. 5.

    et al. Science 324, 1210–1213 (2009).

  6. 6.

    et al. Science 333, 53–58 (2011).

  7. 7.

    et al. Nat. Genet. 43, 745–752 (2011).

  8. 8.

    et al. Genome Res. 22, 142–150 (2012).

  9. 9.

    et al. Nat. Biotechnol. 30, 253–260 (2012).

  10. 10.

    , & PLoS One 6, e25842 (2011).

  11. 11.

    , , & Science 335, 1302 (2012).

  12. 12.

    & Science 335, 1302 (2012).

  13. 13.

    , & Science 335, 1302 (2012).

  14. 14.

    & Bioinformatics 25, 1754–1760 (2009).

  15. 15.

    , , & RNA 12, 1802–1809 (2006).

  16. 16.

    , & Nature 475, 163–165 (2011).

  17. 17.

    & Bioinformatics 26, 1772–1776 (2010).

  18. 18.

    et al. Nucleic Acids Res. 37, e123 (2009).

  19. 19.

    & Brief. Bioinform. 11, 473–483 (2010).

  20. 20.

    et al. Bioinformatics 25, 2078–2079 (2009).

  21. 21.

    et al. Nature 467, 1061–1073 (2010).

Download references

Acknowledgements

We thank E. Levanon and N. Sanjana for critical reading of the manuscript, C. Pan and J. Sun for technical assistance, and T. Gingeras for support. This work is supported by the Stanford University Department of Genetics and the US National Institutes of Health.

Author information

Author notes

    • Gokul Ramaswami
    • , Wei Lin
    •  & Robert Piskol

    These authors contributed equally to this work.

Affiliations

  1. Department of Genetics, Stanford University, Stanford, California, USA.

    • Gokul Ramaswami
    • , Robert Piskol
    • , Meng How Tan
    •  & Jin Billy Li
  2. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

    • Wei Lin
    •  & Carrie Davis

Authors

  1. Search for Gokul Ramaswami in:

  2. Search for Wei Lin in:

  3. Search for Robert Piskol in:

  4. Search for Meng How Tan in:

  5. Search for Carrie Davis in:

  6. Search for Jin Billy Li in:

Contributions

G.R., W.L. and R.P. performed the computational analyses with help from M.H.T. and J.B.L. M.H.T. and G.R. carried out the validation experiments. C.D. generated the GM12878 RNA-seq data. R.P. and J.B.L. wrote the paper with input from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jin Billy Li.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–9, Supplementary Tables 1–5, and Supplementary Notes 1–4

Excel files

  1. 1.

    Supplementary Data 1

    All RNA editing sites identified in GM12878 using our method.

  2. 2.

    Supplementary Data 2

    All RNA editing sites identified in YH using our method.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.1982

Further reading