Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Systematic identification of abundant A-to-I editing sites in the human transcriptome

Abstract

RNA editing by members of the ADAR (adenosine deaminases acting on RNA) family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential for mammalian development. Currently, only a limited number of human ADAR substrates are known, whereas indirect evidence suggests a substantial fraction of all pre-mRNAs being affected. Here we describe a computational search for ADAR editing sites in the human transcriptome, using millions of available expressed sequences. We mapped 12,723 A-to-I editing sites in 1,637 different genes, with an estimated accuracy of 95%, raising the number of known editing sites by two orders of magnitude. We experimentally validated our method by verifying the occurrence of editing in 26 novel substrates. A-to-I editing in humans primarily occurs in noncoding regions of the RNA, typically in Alu repeats. Analysis of the large set of editing sites indicates the role of editing in controlling dsRNA stability.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: ADAR-mediated editing.
Figure 2: Distribution of mismatches between the DNA and the expressed RNA sequences that pass the cleaning algorithm.
Figure 3: Editing in the CFLAR transcript.
Figure 4: Editing in the F11 receptor (JAM1) gene.

References

  1. Polson, A.G., Crain, P.F., Pomerantz, S.C., McCloskey, J.A. & Bass, B.L. The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis. Biochemistry 30, 11507–11514 (1991).

    CAS  Article  Google Scholar 

  2. Tonkin, L.A. et al. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J. 21, 6025–6035 (2002).

    CAS  Article  Google Scholar 

  3. Palladino, M.J., Keegan, L.P., O'Connell, M.A. & Reenan, R.A. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell 102, 437–449 (2000).

    CAS  Article  Google Scholar 

  4. Wang, Q., Khillan, J., Gadue, P. & Nishikura, K. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis. Science 290, 1765–1768 (2000).

    CAS  Article  Google Scholar 

  5. Higuchi, M. et al. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406, 78–81 (2000).

    CAS  Article  Google Scholar 

  6. Yang, J.H. et al. Widespread inosine-containing mRNA in lymphocytes regulated by ADAR1 in response to inflammation. Immunology 109, 15–23 (2003).

    CAS  Article  Google Scholar 

  7. Patterson, J.B. & Samuel, C.E. Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase. Mol. Cell. Biol. 15, 5376–5388 (1995).

    CAS  Article  Google Scholar 

  8. Brusa, R. et al. Early-onset epilepsy and postnatal lethality associated with an editing-deficient GluR-B allele in mice. Science 270, 1677–1680 (1995).

    CAS  Article  Google Scholar 

  9. Gurevich, I. et al. Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims. Neuron 34, 349–356 (2002).

    CAS  Article  Google Scholar 

  10. Kawahara, Y. et al. Glutamate receptors: RNA editing and death of motor neurons. Nature 427, 801 (2004).

    CAS  Article  Google Scholar 

  11. Maas, S., Patt, S., Schrey, M. & Rich, A. Underediting of glutamate receptor GluR-B mRNA in malignant gliomas. Proc. Natl. Acad. Sci. USA 98, 14687–14692 (2001).

    CAS  Article  Google Scholar 

  12. Bass, B.L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817–846 (2002).

    CAS  Article  Google Scholar 

  13. Morse, D.P. & Bass, B.L. Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA. Proc. Natl. Acad. Sci. USA 96, 6048–6053 (1999).

    CAS  Article  Google Scholar 

  14. Hoopengardner, B., Bhalla, T., Staber, C. & Reenan, R. Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832–836 (2003).

    CAS  Article  Google Scholar 

  15. Paul, M.S. & Bass, B.L. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J. 17, 1120–1127 (1998).

    CAS  Article  Google Scholar 

  16. Kikuno, R., Nagase, T., Waki, M. & Ohara, O. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project. Nucleic Acids Res. 30, 166–168 (2002).

    CAS  Article  Google Scholar 

  17. Seeburg, P.H. A-to-I editing: new and old sites, functions and speculations. Neuron 35, 17–20 (2002).

    CAS  Article  Google Scholar 

  18. Boguski, M.S., Lowe, T.M. & Tolstoshev, C.M. dbEST–database for “expressed sequence tags”. Nat. Genet. 4, 332–333 (1993).

    CAS  Article  Google Scholar 

  19. Hillier, L.D. et al. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6, 807–828 (1996).

    CAS  Article  Google Scholar 

  20. Sorek, R., Ast, G. & Graur, D. Alu-containing exons are alternatively spliced. Genome Res. 12, 1060–1067 (2002).

    CAS  Article  Google Scholar 

  21. Morse, D.P., Aruscavage, P.J. & Bass, B.L. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc. Natl. Acad. Sci. USA 99, 7906–7911 (2002).

    CAS  Article  Google Scholar 

  22. Maas, S. et al. Structural requirements for RNA editing in glutamate receptor pre-mRNAs by recombinant double-stranded RNA adenosine deaminase. J. Biol. Chem. 271, 12221–12226 (1996).

    CAS  Article  Google Scholar 

  23. Polson, A.G. & Bass, B.L. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 13, 5701–5711 (1994).

    CAS  Article  Google Scholar 

  24. Lehmann, K.A. & Bass, B.L. Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities. Biochemistry 39, 12875–12884 (2000).

    CAS  Article  Google Scholar 

  25. Kim, U., Wang, Y., Sanford, T., Zeng, Y. & Nishikura, K. Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing. Proc. Natl. Acad. Sci. USA 91, 11457–11461 (1994).

    CAS  Article  Google Scholar 

  26. Higuchi, M. et al. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 75, 1361–1370 (1993).

    CAS  Article  Google Scholar 

  27. Wong, S.K., Sato, S. & Lazinski, D.W. Substrate recognition by ADAR1 and ADAR2. RNA 7, 846–858 (2001).

    CAS  Article  Google Scholar 

  28. Lei, M., Liu, Y. & Samuel, C.E. Adenovirus VAI RNA antagonizes the RNA-editing activity of the ADAR adenosine deaminase. Virology 245, 188–196 (1998).

    CAS  Article  Google Scholar 

  29. Tonkin, L.A. & Bass, B.L. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science 302, 1725 (2003).

    CAS  Article  Google Scholar 

  30. Ausubel, F.M. et al. Current Protocols in Molecular Biology (John Wiley & Sons, Inc., New York, 1987).

    Google Scholar 

  31. Jiang, R. et al. Genome-wide evaluation of the public SNP databases. Pharmacogenomics 4, 779–789 (2003).

    CAS  Article  Google Scholar 

  32. Antonarakis, S.E., Krawczak, M. & Cooper, D.C. in The Genetic Basis of Human Cancer, edn. 2 (eds. Vogelstein, B. & Kinzler, K.W.) 7–41 (McGraw-Hill, New-York, 2002).

    Google Scholar 

Download references

Acknowledgements

We thank A. Diber, E. Shuster and S. Zevin for technical help and P. Akiva, A. Amit and R. Sorek for critical reading of the manuscript. The work of E.Y.L. was done in partial fulfillment of the requirements for a PhD degree from the Sackler Faculty of Medicine, Tel Aviv University, Israel. Part of this work was supported by the Austrian Science Foundation grant SFB1706 to M.J.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Erez Y Levanon.

Ethics declarations

Competing interests

Some authors are past or present employees of Compugen, Ltd.

Supplementary information

Supplementary Fig. 1

Editing in the predicted MGC3329 transcript. (PDF 310 kb)

Supplementary Notes (PDF 32 kb)

Supplementary Methods (PDF 39 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Levanon, E., Eisenberg, E., Yelin, R. et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22, 1001–1005 (2004). https://doi.org/10.1038/nbt996

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt996

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing