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Visualizing adenosine-to-inosine RNA editing in single mammalian cells

Nature Methods volume 14, pages 801804 (2017) | Download Citation

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Abstract

Conversion of adenosine to inosine is a frequent type of RNA editing, but important details about the biology of this conversion remain unknown because of a lack of imaging tools. We developed inoFISH to directly visualize and quantify adenosine-to-inosine-edited transcripts in situ. We found that editing of the GRIA2, EIF2AK2, and NUP43 transcripts is uncorrelated with nuclear localization and paraspeckle association. Further, NUP43 exhibits constant editing levels between single cells, while GRIA2 editing levels vary.

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Change history

  • 20 July 2017

    In the version of this article initially published online, a statement in the introductory paragraph incorrectly implied that deamination leads to defects in hematopoiesis and neurological functions. It is the lack of deamination that causes these defects. The error has been corrected in the print, PDF and HTML versions of this article.

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Acknowledgements

We thank K. Nishikura and M. Sakurai for helpful discussions, and we thank C. Bartman and B. Emert for comments and suggestions. I.A.M. acknowledges support from NIH/NIGMS T32GM007170 (University of Pennsylvania MSTP), NIH/NHGRI T32HG000046 and NIH/NINDS F30NS100595; S.H.R. from NIH 1F32GM120929-01A1; and A.R. from NSF CAREER Award 1350601, NIH New Innovator 1DP2OD008514, NIH/NIBIB R33 EB019767, NIH 4DN U01 HL129998, and NIH Center for Photogenomics RM1 HG007743.

Author information

Affiliations

  1. Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Ian A Mellis
    • , Rohit Gupte
    • , Arjun Raj
    •  & Sara H Rouhanifard
  2. Genomics and Computational Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Ian A Mellis
    •  & Arjun Raj
  3. Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Arjun Raj

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Contributions

S.H.R., I.A.M., and A.R. conceived of the paper; S.H.R. and I.A.M. performed experiments; I.A.M., R.G., and A.R. wrote custom software; I.A.M., S.H.R., and A.R. analyzed the data; I.A.M., S.H.R., and A.R. wrote the paper.

Competing interests

A.R. receives royalties and consulting income from Biosearch Technologies related to Stellaris RNA FISH.

Corresponding author

Correspondence to Sara H Rouhanifard.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Note 1.

  2. 2.

    Supplementary Protocol

    inoFISH Supplementary Protocol.

Excel files

  1. 1.

    Supplementary Table 1

    Sequences of oligonucleotides used.

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DOI

https://doi.org/10.1038/nmeth.4332

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