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

Nature volume 415, pages 810–813 (2002)Cite this article

Abstract

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.

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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.

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References

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

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  Google Scholar 

  7. Beechey, C. V., Cattanach, B. M. & Selley, R. L. Mouse Imprinting Data and References. MRC Mammalian Genetics Unit [online] 〈http://www.mgu.har.mrc.ac.uk/imprinting/imprinting.html〉 (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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  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 

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Acknowledgements

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).

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Authors and Affiliations

  1. Department of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands

    Frank Sleutels & Ronald Zwart

  2. ÖAW Institute of Molecular Biology, Billrothstrasse 11, Salzburg, A5020, Austria

    Denise P. Barlow

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  1. Frank Sleutels
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  2. Ronald Zwart
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  3. Denise P. Barlow
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Correspondence to Denise P. Barlow.

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Sleutels, F., Zwart, R. & Barlow, D. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810–813 (2002). https://doi.org/10.1038/415810a

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