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

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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.

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Figure 1: A computational framework to identify RNA editing sites in Alu and non-Alu regions.
Figure 2: Editing of many non-Alu sites appears to be dependent on nearby edited Alu sites.

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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.

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Author notes

  1. Gokul Ramaswami, Wei Lin and Robert Piskol: These authors contributed equally to this work.

Authors and 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. Gokul Ramaswami
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  2. Wei Lin
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  3. Robert Piskol
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  4. Meng How Tan
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  5. Carrie Davis
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  6. Jin Billy Li
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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.

Corresponding author

Correspondence to Jin Billy Li.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9, Supplementary Tables 1–5, and Supplementary Notes 1–4 (PDF 2511 kb)

Supplementary Data 1

All RNA editing sites identified in GM12878 using our method. (XLSX 8161 kb)

Supplementary Data 2

All RNA editing sites identified in YH using our method. (XLSX 47856 kb)

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Ramaswami, G., Lin, W., Piskol, R. et al. Accurate identification of human Alu and non-Alu RNA editing sites. Nat Methods 9, 579–581 (2012). https://doi.org/10.1038/nmeth.1982

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

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