Skip to main content

Thank you for visiting 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.

The non-coding Air RNA is required for silencing autosomal imprinted genes


In genomic imprinting, one of the two parental alleles of an autosomal gene is silenced epigenetically by a cis-acting mechanism1,2. A bidirectional silencer for a 400-kilobase region that contains three imprinted, maternally expressed protein-coding genes (Igf2r/Slc22a2/Slc22a3) has been shown by targeted deletion to be located in a sequence of 3.7 kilobases3,4,5, which also contains the promoter for the imprinted, paternally expressed non-coding Air RNA6. Expression of Air is correlated with repression of all three genes on the paternal allele5; however, Air RNA overlaps just one of these genes in an antisense orientation6. Here we show, by inserting a polyadenylation signal that truncates 96% of the RNA transcript, that Air RNA is required for silencing. The truncated Air allele maintains imprinted expression and methylation of the Air promoter, but shows complete loss of silencing of the Igf2r/Slc22a2/Slc22a3 gene cluster on the paternal chromosome. Our results indicate that non-coding RNAs have an active role in genomic imprinting.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Generation of the Air-T allele.
Figure 2: The Air-T allele truncates the Air RNA.
Figure 3: The Air-T allele is imprinted.
Figure 4: Loss of paternal silencing on the Air-T allele.


  1. Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nature Rev. Genet. 2, 21–32 (2001).

    CAS  Article  Google Scholar 

  2. Sleutels, F. & Barlow, D. P. in Homology Effects (eds Wu, C.-t. & Dunlap, C.) (Academic, San Diego, in the press).

  3. Wutz, A. et al. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745–749 (1997).

    CAS  Article  Google Scholar 

  4. Wutz, A. et al. Non-imprinted Igf2r expression decreases growth and rescues the Tme mutation in mice. Development 128, 1881–1887 (2001).

    CAS  Google Scholar 

  5. Zwart, R., Sleutels, F., Wutz, A., Schinkel, A. H. & Barlow, D. P. Bidirectional action of the Igf2r imprint control element on upstream and downstream imprinted genes. Genes Dev. 15, 2361–2366 (2001).

    CAS  Article  Google Scholar 

  6. Lyle, R. et al. The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nature Genet. 25, 19–21 (2000).

    CAS  Article  Google Scholar 

  7. Beechey, C. V., Cattanach, B. M. & Selley, R. L. Mouse Imprinting Data and References. MRC Mammalian Genetics Unit [online] 〈〉 (2000).

  8. Schmidt, J. V., Levorse, J. M. & Tilghman, S. M. Enhancer competition between H19 and Igf2 does not mediate their imprinting. Proc. Natl Acad. Sci. USA 96, 9733–9738 (1999).

    CAS  Article  Google Scholar 

  9. Hark, A. T. et al. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405, 486–489 (2000).

    CAS  Article  Google Scholar 

  10. Constancia, M. et al. Deletion of a silencer element in Igf2 results in loss of imprinting independent of H19. Nature Genet. 26, 203–206 (2000).

    CAS  Article  Google Scholar 

  11. Bell, A. C. & Felsenfeld, G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482–485 (2000).

    CAS  Article  Google Scholar 

  12. Reik, W. & Murrell, A. Genomic imprinting. Silence across the border. Nature 405, 408–409 (2000).

    CAS  Article  Google Scholar 

  13. Wang, Z. Q., Fun, M. R., Barlow, D. P. & Wagner, E. F. Regulation of embryonic growth and lysosomal targeting by the imprinted Igf2/Mpr gene. Nature 372, 464–467 (1994).

    CAS  Article  Google Scholar 

  14. Sleutels, F. & Barlow, D. P. Investigation of elements sufficient to imprint the mouse Air promoter. Mol. Cell. Biol. 21, 5008–5017. (2001).

    CAS  Article  Google Scholar 

  15. Wroe, S. F. et al. An imprinted transcript, antisense to Nesp, adds complexity to the cluster of imprinted genes at the mouse Gnas locus. Proc. Natl Acad. Sci. USA 97, 3342–3346 (2000).

    CAS  Article  Google Scholar 

  16. Lee, Y. J. et al. Mit1/Lb9 and Copg2, new members of mouse imprinted genes closely linked to Peg1/Mest1. FEBS Lett. 472, 230–234 (2000).

    CAS  Article  Google Scholar 

  17. Rougeulle, C., Cardoso, C., Fontes, M., Colleaux, L. & Lalande, M. An imprinted antisense RNA overlaps UBE3A and a second maternally expressed transcript. Nature Genet. 19, 15–16 (1998).

    CAS  Article  Google Scholar 

  18. Smilinich, N. J. et al. A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc. Natl Acad. Sci. USA 96, 8064–8069 (1999).

    CAS  Article  Google Scholar 

  19. Avner, P. & Heard, E. X-chromosome inactivation: counting, choice and initiation. Nature Rev. Genet. 2, 59–67 (2001).

    CAS  Article  Google Scholar 

  20. Clemson, C. M., McNeil, J. A., Willard, H. F. & Lawrence, J. B. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J. Cell Biol. 132, 259–275 (1996).

    CAS  Article  Google Scholar 

  21. Lee, J. T., Strauss, W. M., Dausman, J. A. & Jaenisch, R. A 450 kb transgene displays properties of the mammalian X-inactivation center. Cell 86, 83–94 (1996).

    CAS  Article  Google Scholar 

  22. Sheardown, S. A. et al. Stabilization of Xist RNA mediates initiation of X chromosome inactivation. Cell 91, 99–107 (1997).

    CAS  Article  Google Scholar 

  23. Wutz, A. & Jaenisch, R. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol. Cell 5, 695–705 (2000).

    CAS  Article  Google Scholar 

  24. Lyon, M. F. Imprinting and X-chromosome inactivation. Results Probl. Cell Differ. 25, 73–90 (1999).

    CAS  Article  Google Scholar 

  25. Graves, J. A. Mammals that break the rules: genetics of marsupials and monotremes. Annu. Rev. Genet. 30, 233–260 (1996).

    CAS  Article  Google Scholar 

  26. O'Gorman, S., Dagenais, N. A., Qian, M. & Marchuk, Y. Protamine-Cre recombinase transgenes efficiently recombine target sequences in the male germ line of mice, but not in embryonic stem cells. Proc. Natl Acad. Sci. USA 94, 14602–14607 (1997).

    CAS  Article  Google Scholar 

  27. Hogan, B. L. M., Beddington, R. S. P., Costantini, F. & Lacy, E. Manipulating the Mouse Embryo (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1994).

    Google Scholar 

Download references


We thank K. van Veen, K. van het Wout, P. Krimpenfort for help in generating mice; S. Greven, T. Maidment and N. Bosnie for care of the mice; A. Berns, H. te Riele, M. van Lohuizen, R. Beijersbergen, P. Borst and A. Frischauf for comments; and A. Berns for help and encouragement. This research was supported by the Dutch Cancer Society (KWF).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Denise P. Barlow.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Sleutels, F., Zwart, R. & Barlow, D. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810–813 (2002).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


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.


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