Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides

Abstract

EUKARYOTIC ribosomal RNAs are post-transcriptionally modified by methylation at the ribose sugar of specific nucleotides1. This takes place in the nucleolus and involves a family of small nucleolar RNAs (snoRNAs) with long regions (10–21 nucleotides) complementary to rRNA sequences spanning the methylation site2–4—a complementary snoRNA is required for methylation at a specific site5. Here we show that altering the sequence of the snoRNA is sufficient to change the specificity of methylation. Mammalian cells transfected with a snoRNA engineered to be complementary to an arbitrary rRNA sequence direct the methylation of the predicted nucleotide in that sequence. We have further identified structural features, both of the guide and substrate RNA, required for methylation and have used these to design an exogenous transcript, devoid of rRNA sequence, that is site-specifically methylated when co-expressed with an appropriate guide snoRNA. Endogenous non-ribosomal RNA can thus be targeted, possibly providing a highly selective tool for the alteration of gene expression at the post-transcriptional level.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1

    Maden, B. E. H. Prog. Nucleic Acid Res. Mol. Biol. 39, 241–301 (1990).

    CAS  Article  Google Scholar 

  2. 2

    Bachellerie, J.-P. et al. Trends Biochem. Sci. 20, 261–264 (1995).

    CAS  Article  Google Scholar 

  3. 3

    Maxwell, E. S. & Fournier, M. J. Annu. Rev. Biochem. 35, 897–934 (1995).

    Article  Google Scholar 

  4. 4

    Nicoloso, M., Qu, L. H., Michot, B. & Bachellerie, J. P. J. Mol. Biol. 260, 178–195 (1996).

    CAS  Article  Google Scholar 

  5. 5

    Kiss-Laszlo, Z. et al. Cell 85, 1077–1088 (1996).

    CAS  Article  Google Scholar 

  6. 6

    Nicoloso, M. et al. Mol. Cell. Biol. 14, 5766–5776 (1994).

    CAS  Article  Google Scholar 

  7. 7

    Maden, B. E. H. & Salim, M. J. Mol. Biol. 88, 133–164 (1974).

    CAS  Article  Google Scholar 

  8. 8

    Miller, K. S., Zbrzezna, V. & Pogo, A. O. J. Mol. Biol. 177, 343–368 (1984).

    CAS  Article  Google Scholar 

  9. 9

    Tollervey, D. EMBO J. 6, 4169–4175 (1987).

    CAS  Article  Google Scholar 

  10. 10

    Perry, R. P. & Kelley, D. E. J. Cell Physiol. 76, 127–140 (1970).

    CAS  Article  Google Scholar 

  11. 11

    Bachellerie, J. P. et al. Biochem. Cell Biol. 73, 835–843 (1995).

    CAS  Article  Google Scholar 

  12. 12

    Cavaillé, J. & Bachellerie, J. P. Biochimie 78, 443–456 (1996).

    Article  Google Scholar 

  13. 13

    Warner, J. R. J. Mol. Biol. 19, 383–398 (1966).

    CAS  Article  Google Scholar 

  14. 14

    Caffarelli, E. et al. EMBO J. 15, 1121–1131 (1996).

    CAS  Article  Google Scholar 

  15. 15

    Tycowski, K. T., Shu, M.-D. & Steitz, J. A. Nature 379, 464–466 (1996).

    ADS  CAS  Article  Google Scholar 

  16. 16

    Hadjiolova, K. et al. Mol. Cell. Biol. 14, 4044–4056 (1994).

    CAS  Article  Google Scholar 

  17. 17

    Steitz, J. A. & Tycowski, K. T. Science 270, 1626–1627 (1995).

    ADS  CAS  Article  Google Scholar 

  18. 18

    Caboche, M. & Bachellerie, J. P. Eur. J. Biochem. 74, 19–29 (1977).

    CAS  Article  Google Scholar 

  19. 19

    Tollervey, D. et al. Cell 72, 443–457 (1993).

    CAS  Article  Google Scholar 

  20. 20

    Bond, V. C. & Wold, B. Mol. Cell. Biol. 13, 3221–3230 (1993).

    CAS  Article  Google Scholar 

  21. 21

    Schneiter, R., Kadowaki, T. & Tartakoff, A. M. Mol. Biol. Cell 6, 357–370 (1995).

    CAS  Article  Google Scholar 

  22. 22

    Moore, M. J. & Sharp, P. M. Science 256, 992–997 (1992).

    ADS  CAS  Article  Google Scholar 

  23. 23

    Bardwell, V. J. et al. Cell 65, 125–133 (1991).

    CAS  Article  Google Scholar 

  24. 24

    Cattaneo, R. Curr. Biol. 4, 134–136 (1994).

    CAS  Article  Google Scholar 

  25. 25

    Kunkel, T. A. Proc. Natl Acad. Sci. USA 82, 488–492 (1985).

    ADS  CAS  Article  Google Scholar 

  26. 26

    Branch, A. D., Benenfeld, B. J. & Robertson, H. D. Meth. Enzymol. 180, 130–154 (1989).

    CAS  Article  Google Scholar 

  27. 27

    Bourbon, H. M. & Amalric, F. Gene 88, 187–196 (1990).

    CAS  Article  Google Scholar 

  28. 28

    Reimer, G. et al. Arthritis Rheum. 30, 793–800 (1987).

    CAS  Article  Google Scholar 

  29. 29

    Chomczynski, P. & Sacchi, N. Anal. Biochem. 162, 156–159 (1987).

    CAS  Article  Google Scholar 

  30. 30

    Maden, B. E. H. et al. Biochimie 77, 22–29 (1995).

    CAS  Article  Google Scholar 

Download references

Author information

Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Cavaillé, J., Nicoloso, M. & Bachellerie, JP. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383, 732–735 (1996). https://doi.org/10.1038/383732a0

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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