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

Rosenberg, Brad R, Hamilton, Claire E, Mwangi, Michael M, Dewell, Scott, Papavasiliou, F Nina·2011·Nature Structural & Molecular Biology
DOI 10.1038/nsmb.1975PMC PMC3075553
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  • A3A prefers for an UCa/u trinucleotide motif and A1 + A1CF prefers ACu/a motif.

    “Analysis of the sequence contexts around the significant target C sites (with ± 5 nucleotides from target C) showed that A3A prefers for an UCa/u trinucleotide motif and A1 + A1CF prefers ACu/a motif (Fig. 2A), which is consistent with the reported motif preference for RNA editing by A3A and A125,31.”

    From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [31]

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Research works printed but not linked: 56

  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). · DOI
  2. Gray, M.W. Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55, 227–233 (2003). · DOI
  3. Pullirsch, D. & Jantsch, M.F. Proteome diversification by adenosine to inosine RNA-editing. RNA Biol. 7, 205–212 (2010). · DOI
  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). · DOI
  5. Prasanth, K.V. et al. Regulating gene expression through RNA nuclear retention. Cell 123, 249–263 (2005). · DOI
  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). · DOI
  7. Chen, L.-L., DeCerbo, J.N. & Carmichael, G.G. Alu element-mediated gene silencing. EMBO J. 27, 1694–1705 (2008). · DOI
  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). · DOI
  9. Powell, L.M. et al. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50, 831–840 (1987). · DOI
  10. Teng, B., Burant, C.F. & Davidson, N.O. Molecular cloning of an apolipoprotein B messenger RNA editing protein. Science 260, 1816–1819 (1993). · DOI · Paper page
  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). · DOI
  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). · DOI
  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). · DOI
  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). · DOI
  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). · DOI
  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). · DOI · Paper page
  17. Shah, R.R. et al. Sequence requirements for the editing of apolipoprotein B mRNA. J. Biol. Chem. 266, 16301–16304 (1991). · DOI
  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). · DOI
  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). · DOI
  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). · DOI
  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). · DOI
  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). · DOI
  23. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008). · DOI · Paper page
  24. 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). · DOI · Paper page
  25. 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). · DOI
  26. 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). · DOI
  27. 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). · DOI
  28. 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). · DOI · Paper page
  29. 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). · DOI
  30. Davidson, N.O. The challenge of target sequence specificity in C→U RNA editing. J. Clin. Invest. 109, 291–294 (2002). · DOI
  31. Bass, B.L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817–846 (2002). · DOI
  32. 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). · DOI
  33. 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).
  34. 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). · DOI
  35. 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). · DOI · Paper page
  36. 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). · DOI
  37. 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). · DOI
  38. 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). · DOI
  39. 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). · DOI
  40. Levanon, E.Y. et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001–1005 (2004). · DOI
  41. Osenberg, S., Dominissini, D., Rechavi, G. & Eisenberg, E. Widespread cleavage of A-to-I hyperediting substrates. RNA 15, 1632–1639 (2009). · DOI
  42. Borchert, G.M. et al. Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum. Mol. Genet. 18, 4801–4807 (2009). · DOI
  43. Liang, H. & Landweber, L.F. Hypothesis: RNA editing of microRNA target sites in humans? RNA 13, 463–467 (2007). · DOI
  44. Barreau, C., Paillard, L. & Osborne, H.B. AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res. 33, 7138–7150 (2005). · DOI · Paper page
  45. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007). · DOI · Paper page
  46. 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). · DOI
  47. 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). · DOI
  48. 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). · DOI
  49. 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). · DOI
  50. 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). · DOI · Paper page
  51. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). · DOI
  52. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). · DOI · Paper page
  53. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008). · DOI · Paper page
  54. 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). · DOI
  55. Crooks, G.E., Hon, G., Chandonia, J.-M. & Brenner, S.E. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004). · DOI
  56. 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). · DOI

Cited by

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Metadata

Authors
Rosenberg, B. R., Hamilton, C. E., Mwangi, M. M., Dewell, S., & Papavasiliou, F. N.
Venue
Nature Structural & Molecular Biology
Publisher
Springer Science and Business Media LLC
Published
2011-01-23
Volume
18
Issue
2
Pages
230-236
ISSN
  • 1545-9993
  • 1545-9985
DOI
10.1038/nsmb.1975
PMC
PMC3075553
Cited by
232
References
3
Language
en
Update notices
erratum (2012-03-05)
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