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.

  • Resource
  • Published:

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

A Corrigendum to this article was published on 05 March 2012

This article has been updated

Abstract

Apolipoprotein B–editing enzyme, catalytic polypeptide-1 (APOBEC1) is a cytidine deaminase initially identified by its activity in converting a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts in the small intestine. Editing results in the translation of a truncated apoB isoform with distinct functions in lipid transport. To address the possibility that APOBEC1 edits additional mRNAs, we developed a transcriptome-wide comparative RNA sequencing (RNA-Seq) screen. We identified and validated 32 previously undescribed mRNA targets of APOBEC1 editing, all of which are located in AU-rich segments of transcript 3′ untranslated regions (3′ UTRs). Further analysis established several characteristic sequence features of editing targets, which were predictive for the identification of additional APOBEC1 substrates. The transcriptomics approach to RNA editing presented here dramatically expands the list of APOBEC1 mRNA editing targets and reveals a novel cellular mechanism for the modification of transcript 3′ UTRs.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Comparative RNA-Seq screen for APOBEC1 mRNA-editing targets.
Figure 2: Validation of APOBEC1 mRNA-editing targets.
Figure 3: Sequence features of APOBEC1 editing sites.
Figure 4: APOBEC1 mRNA-editing targets share a characteristic sequence motif.
Figure 5: Sequence pattern prediction of APOBEC1 mRNA-editing targets.

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

Change history

  • 14 December 2011

    In the version of this article initially published, financial support from the Starr Foundation was not acknowledged. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Grosjean, H. et al. Enzymatic conversion of adenosine to inosine and to N1-methylinosine in transfer RNAs: a review. Biochimie 78, 488–501 (1996).

    Article  CAS  PubMed  Google Scholar 

  2. Gray, M.W. Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55, 227–233 (2003).

    Article  CAS  PubMed  Google Scholar 

  3. Pullirsch, D. & Jantsch, M.F. Proteome diversification by adenosine to inosine RNA-editing. RNA Biol. 7, 205–212 (2010).

    Article  CAS  PubMed  Google Scholar 

  4. Kumar, M. & Carmichael, G.G. Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts. Proc. Natl. Acad. Sci. USA 94, 3542–3547 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Prasanth, K.V. et al. Regulating gene expression through RNA nuclear retention. Cell 123, 249–263 (2005).

    Article  CAS  PubMed  Google Scholar 

  6. Zhang, Z. & Carmichael, G.G. The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell 106, 465–475 (2001).

    Article  CAS  PubMed  Google Scholar 

  7. Chen, L.-L., DeCerbo, J.N. & Carmichael, G.G. Alu element-mediated gene silencing. EMBO J. 27, 1694–1705 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen, S.H. et al. Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 238, 363–366 (1987).

    Article  CAS  PubMed  Google Scholar 

  9. Powell, L.M. et al. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50, 831–840 (1987).

    Article  CAS  PubMed  Google Scholar 

  10. Teng, B., Burant, C.F. & Davidson, N.O. Molecular cloning of an apolipoprotein B messenger RNA editing protein. Science 260, 1816–1819 (1993).

    Article  CAS  PubMed  Google Scholar 

  11. Navaratnam, N. et al. The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. J. Biol. Chem. 268, 20709–20712 (1993).

    CAS  PubMed  Google Scholar 

  12. Conticello, S.G., Thomas, C.J.F., Petersen-Mahrt, S.K. & Neuberger, M.S. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol. Biol. Evol. 22, 367–377 (2005).

    Article  CAS  PubMed  Google Scholar 

  13. Navaratnam, N. et al. Evolutionary origins of apoB mRNA editing: catalysis by a cytidine deaminase that has acquired a novel RNA-binding motif at its active site. Cell 81, 187–195 (1995).

    Article  CAS  PubMed  Google Scholar 

  14. Anant, S., MacGinnitie, A.J. & Davidson, N.O. apobec-1, the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme, is a novel RNA-binding protein. J. Biol. Chem. 270, 14762–14767 (1995).

    Article  CAS  PubMed  Google Scholar 

  15. Mehta, A., Kinter, M.T., Sherman, N.E. & Driscoll, D.M. Molecular cloning of apobec-1 complementation factor, a novel RNA-binding protein involved in the editing of apolipoprotein B mRNA. Mol. Cell. Biol. 20, 1846–1854 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Lellek, H. et al. Purification and molecular cloning of a novel essential component of the apolipoprotein B mRNA editing enzyme-complex. J. Biol. Chem. 275, 19848–19856 (2000).

    Article  CAS  PubMed  Google Scholar 

  17. Shah, R.R. et al. Sequence requirements for the editing of apolipoprotein B mRNA. J. Biol. Chem. 266, 16301–16304 (1991).

    CAS  PubMed  Google Scholar 

  18. Backus, J.W. & Smith, H.C. Apolipoprotein B mRNA sequences 3′ of the editing site are necessary and sufficient for editing and editosome assembly. Nucleic Acids Res. 19, 6781–6786 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hirano, K. et al. Targeted disruption of the mouse apobec-1 gene abolishes apolipoprotein B mRNA editing and eliminates apolipoprotein B48. J. Biol. Chem. 271, 9887–9890 (1996).

    Article  CAS  PubMed  Google Scholar 

  20. Morrison, J.R. et al. Apolipoprotein B RNA editing enzyme-deficient mice are viable despite alterations in lipoprotein metabolism. Proc. Natl. Acad. Sci. USA 93, 7154–7159 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Yamanaka, S. et al. Apolipoprotein B mRNA-editing protein induces hepatocellular carcinoma and dysplasia in transgenic animals. Proc. Natl. Acad. Sci. USA 92, 8483–8487 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Li, J.B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210–1213 (2009).

    Article  CAS  PubMed  Google Scholar 

  23. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).

    Article  CAS  PubMed  Google Scholar 

  25. Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956–960 (2008).

    Article  CAS  PubMed  Google Scholar 

  26. Heap, G.A. et al. Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum. Mol. Genet. 19, 122–134 (2010).

    Article  CAS  PubMed  Google Scholar 

  27. Chepelev, I., Wei, G., Tang, Q. & Zhao, K. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res. 37, e106 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Yamanaka, S., Poksay, K.S., Driscoll, D.M. & Innerarity, T.L. Hyperediting of multiple cytidines of apolipoprotein B mRNA by APOBEC-1 requires auxiliary protein(s) but not a mooring sequence motif. J. Biol. Chem. 271, 11506–11510 (1996).

    Article  CAS  PubMed  Google Scholar 

  29. Sowden, M., Hamm, J.K. & Smith, H.C. Overexpression of APOBEC-1 results in mooring sequence-dependent promiscuous RNA editing. J. Biol. Chem. 271, 3011–3017 (1996).

    Article  CAS  PubMed  Google Scholar 

  30. Sowden, M.P., Eagleton, M.J. & Smith, H.C. Apolipoprotein B RNA sequence 3′ of the mooring sequence and cellular sources of auxiliary factors determine the location and extent of promiscuous editing. Nucleic Acids Res. 26, 1644–1652 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Davidson, N.O. The challenge of target sequence specificity in C→U RNA editing. J. Clin. Invest. 109, 291–294 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  33. Beale, R.C.L. et al. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. J. Mol. Biol. 337, 585–596 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994).

    CAS  PubMed  Google Scholar 

  35. Backus, J.W. & Smith, H.C. Three distinct RNA sequence elements are required for efficient apolipoprotein B (apoB) RNA editing in vitro. Nucleic Acids Res. 20, 6007–6014 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Duret, L., Dorkeld, F. & Gautier, C. Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res. 21, 2315–2322 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hadjiagapiou, C., Giannoni, F., Funahashi, T., Skarosi, S.F. & Davidson, N.O. Molecular cloning of a human small intestinal apolipoprotein B mRNA editing protein. Nucleic Acids Res. 22, 1874–1879 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Lau, P.P., Zhu, H.J., Baldini, A., Charnsangavej, C. & Chan, L. Dimeric structure of a human apolipoprotein B mRNA editing protein and cloning and chromosomal localization of its gene. Proc. Natl. Acad. Sci. USA 91, 8522–8526 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Mukhopadhyay, D. et al. C→U editing of neurofibromatosis 1 mRNA occurs in tumors that express both the type II transcript and apobec-1, the catalytic subunit of the apolipoprotein B mRNA-editing enzyme. Am. J. Hum. Genet. 70, 38–50 (2002).

    Article  CAS  PubMed  Google Scholar 

  41. Skuse, G.R., Cappione, A.J., Sowden, M., Metheny, L.J. & Smith, H.C. The neurofibromatosis type I messenger RNA undergoes base-modification RNA editing. Nucleic Acids Res. 24, 478–485 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Lomeli, H. et al. Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science 266, 1709–1713 (1994).

    Article  CAS  PubMed  Google Scholar 

  43. Levanon, E.Y. et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001–1005 (2004).

    Article  CAS  PubMed  Google Scholar 

  44. Osenberg, S., Dominissini, D., Rechavi, G. & Eisenberg, E. Widespread cleavage of A-to-I hyperediting substrates. RNA 15, 1632–1639 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Borchert, G.M. et al. Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum. Mol. Genet. 18, 4801–4807 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Liang, H. & Landweber, L.F. Hypothesis: RNA editing of microRNA target sites in humans? RNA 13, 463–467 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Barreau, C., Paillard, L. & Osborne, H.B. AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res. 33, 7138–7150 (2005).

    Article  CAS  PubMed  Google Scholar 

  48. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Kendrick, J.S., Chan, L. & Higgins, J.A. Superior role of apolipoprotein B48 over apolipoprotein B100 in chylomicron assembly and fat absorption: an investigation of apobec-1 knock-out and wild-type mice. Biochem. J. 356, 821–827 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Hirano, K., Min, J., Funahashi, T. & Davidson, N.O. Cloning and characterization of the rat apobec-1 gene: a comparative analysis of gene structure and promoter usage in rat and mouse. J. Lipid Res. 38, 1103–1119 (1997).

    CAS  PubMed  Google Scholar 

  51. Nakamuta, M. et al. Alternative mRNA splicing and differential promoter utilization determine tissue-specific expression of the apolipoprotein B mRNA-editing protein (Apobec1) gene in mice. Structure and evolution of Apobec1 and related nucleoside/nucleotide deaminases. J. Biol. Chem. 270, 13042–13056 (1995).

    Article  CAS  PubMed  Google Scholar 

  52. Xie, Y., Nassir, F., Luo, J., Buhman, K. & Davidson, N.O. Intestinal lipoprotein assembly in apobec-1−/− mice reveals subtle alterations in triglyceride secretion coupled with a shift to larger lipoproteins. Am. J. Physiol. Gastrointest. Liver Physiol. 285, G735–G746 (2003).

    Article  CAS  PubMed  Google Scholar 

  53. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  56. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Taylor, J., Schenck, I., Blankenberg, D. & Nekrutenko, A. Using galaxy to perform large-scale interactive data analyses. Curr. Protoc. Bioinformatics, 19:10.5.1–10.5.25 (2007).

  58. Crooks, G.E., Hon, G., Chandonia, J.-M. & Brenner, S.E. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Marass, F. & Upton, C. Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences. BMC Res Notes 2, 14 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank C. Rice, H. Smith, D. Licatalosi and E. Fritz for critical reading of this manuscript; R. Darnell for discussion and suggestions; and G. Livshits for immunofluorescence assistance. This was supported by the Cancer Research Institute (training grants to B.R.R. and C.E.H.), by the National Institutes of Health (Medical Scientist Training Program grant GM07739 to B.R.R. and C.E.H.) and by a pilot grant through the Rockefeller Clinical and Translational Science Award program (National Institutes of Health National Center for Research Resources grant UL1RR024143 to F.N.P.). This work was supported by the Starr Foundation.

Author information

Authors and Affiliations

Authors

Contributions

B.R.R. and F.N.P. conceived of and designed the work presented; B.R.R. is responsible for data presented in Figures 1, 2, 3, 4 and 5; C.E.H. contributed data to Figure 5 and the Supplementary Figures M.M.M. is responsible for the statistical analysis underlying Figure 3 and Supplementary Figure 5; S.D. provided bioinformatics training and support; and B.R.R. and F.N.P. wrote the manuscript with considerable input from M.M.M., C.E.H. and S.D.

Corresponding author

Correspondence to F Nina Papavasiliou.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–3, 5 and 6 and Supplementary Methods (PDF 8464 kb)

Supplementary Table 4

APOBEC1 Sequence Pattern in RefSeq Transcripts. (XLS 84 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rosenberg, B., Hamilton, C., Mwangi, M. et al. Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs. Nat Struct Mol Biol 18, 230–236 (2011). https://doi.org/10.1038/nsmb.1975

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1975

This article is cited by

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