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An intron with a constitutive transport element is retained in a Tap messenger RNA

Nature volume 443, pages 234–237 (2006)Cite this article

Abstract

Alternative splicing is a key factor contributing to genetic diversity and evolution1. Intron retention, one form of alternative splicing, is common in plants2 but rare in higher eukaryotes3,4,5,6,7,8, because messenger RNAs with retained introns are subject to cellular restriction at the level of cytoplasmic export and expression9,10. Often, retention of internal introns restricts the export of these mRNAs and makes them the targets for degradation by the cellular nonsense-mediated decay machinery if they contain premature stop codons11,12. In fact, many of the database entries for complementary DNAs with retained introns represent them as artefacts that would not affect the proteome11. Retroviruses are important model systems in studies of regulation of RNAs with retained introns, because their genomic and mRNAs contain one or more unspliced introns10. For example, Mason–Pfizer monkey virus overcomes cellular restrictions by using a cis-acting RNA element known as the constitutive transport element (CTE)13. The CTE interacts directly with the Tap protein (also known as nuclear RNA export factor 1, encoded by NXF1), which is thought to be a principal export receptor for cellular mRNA14, leading to the hypothesis that cellular mRNAs with retained introns use cellular CTE equivalents to overcome restrictions to their expression10. Here we show that the Tap gene contains a functional CTE in its alternatively spliced intron 10. Tap mRNA containing this intron is exported to the cytoplasm and is present in polyribosomes. A small Tap protein is encoded by this mRNA and can be detected in human and monkey cells. Our results indicate that Tap regulates expression of its own intron-containing RNA through a CTE-mediated mechanism. Thus, CTEs are likely to be important elements that facilitate efficient expression of mammalian mRNAs with retained introns.

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Figure 1: Genomic organization of the human Tap gene and comparison of the Tap -CTE and MPMV-CTE.
Figure 2: Tap intron 10 contains a functional CTE.
Figure 3: Expression of Tap mRNA retaining intron 10 and a small Tap protein.
Figure 4: RNA and protein expression from wild-type and CTE-mutated Tap minigene constructs.

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Acknowledgements

We thank J. Morgenegg and F.-F. Chen for technical support, and J. Swartz, A. Ward and S. Raman for comments on the manuscript. This work was supported by grants from the National Institutes of Health (to M.-L.H. and to D.R.). Salary support for M.-L.H. and D.R. was provided by the Charles H. Ross Jr and Myles H. Thaler Endowments at the University of Virginia. Author Contributions Y.L. and Y.-c.B. contributed equally to this work.

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  1. Myles H. Thaler Center for AIDS & Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia, 22908, USA

    Ying Li, Yeou-cherng Bor, Yukiko Misawa, Yuming Xue, David Rekosh & Marie-Louise Hammarskjöld

  2. Human Retrovirus Research and Department of Microbiology, University of Virginia,

    Ying Li, Yeou-cherng Bor, Yukiko Misawa, Yuming Xue, David Rekosh & Marie-Louise Hammarskjöld

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Correspondence to Marie-Louise Hammarskjöld.

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Supplementary information

Supplementary Figure 1

Alignment of tap-CTE, MPMV-CTE, and mouse nxf1 gene on chromosome 19. (PDF 322 kb)

Supplementary Figure 2

Expression of p24 in supernatants from transfected 293T cells. (PDF 123 kb)

Supplementary Figure 3

Sucrose gradient analysis of Tap mRNA from 293T cells in the presence of 15 mM EDTA. (PDF 243 kb)

Supplementary Notes

This file contains Supplementary Methods and Supplementary Figure Legends. (DOC 36 kb)

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Li, Y., Bor, Yc., Misawa, Y. et al. An intron with a constitutive transport element is retained in a Tap messenger RNA. Nature 443, 234–237 (2006). https://doi.org/10.1038/nature05107

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