A stress-responsive RNA switch regulates VEGFA expression

Abstract

Ligand binding to structural elements in the non-coding regions of messenger RNA modulates gene expression1,2. Ligands such as free metabolites or other small molecules directly bind and induce conformational changes in regulatory RNA elements known as riboswitches1,2,3,4. Other types of RNA switches are activated by complexed metabolites—for example, RNA-ligated metabolites such as aminoacyl-charged transfer RNA in the T-box system5, or protein-bound metabolites in the glucose- or amino-acid-stimulated terminator-anti-terminator systems6,7. All of these switch types are found in bacteria, fungi and plants8,9,10. Here we report an RNA switch in human vascular endothelial growth factor-A (VEGFA, also known as VEGF) mRNA 3′ untranslated region (UTR) that integrates signals from interferon (IFN)-γ and hypoxia to regulate VEGFA translation in myeloid cells. Analogous to riboswitches, the VEGFA 3′ UTR undergoes a binary conformational change in response to environmental signals. However, the VEGFA 3′ UTR switch is metabolite-independent, and the conformational change is dictated by mutually exclusive, stimulus-dependent binding of proteins, namely, the IFN-γ-activated inhibitor of translation complex11,12 and heterogeneous nuclear ribonucleoprotein L (HNRNPL, also known as hnRNP L). We speculate that the VEGFA switch represents the founding member of a family of signal-mediated, protein-dependent RNA switches that evolved to regulate gene expression in multicellular animals in which the precise integration of disparate inputs may be more important than the rapidity of response.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Suppression of GAIT-mediated translation silencing of VEGFA by hypoxia.
Figure 2: HNRNPL binding to HSR restores VEGFA translation in hypoxia.
Figure 3: HNRNPL is regulated by stimulus-dependent proteasomal degradation.
Figure 4: Protein-dependent switching of the VEGFA 3′ UTR HSR.

References

  1. 1

    Mandal, M. & Breaker, R. R. Gene regulation by riboswitches. Nature Rev. Mol. Cell Biol. 5, 451–463 (2004)

    CAS  Article  Google Scholar 

  2. 2

    Grundy, F. J. & Henkin, T. M. Regulation of gene expression by effectors that bind to RNA. Curr. Opin. Microbiol. 7, 126–131 (2004)

    CAS  Article  Google Scholar 

  3. 3

    Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002)

    CAS  ADS  Article  Google Scholar 

  4. 4

    Cromie, M. J., Shi, Y., Latifi, T. & Groisman, E. A. An RNA sensor for intracellular Mg2+ . Cell 125, 71–84 (2006)

    CAS  Article  Google Scholar 

  5. 5

    Grundy, F. J. & Henkin, T. M. tRNA as a positive regulator of transcription antitermination in B. subtilis . Cell 74, 475–482 (1993)

    CAS  Article  Google Scholar 

  6. 6

    Merino, E., Babitzke, P. & Yanofsky, C. trp RNA-binding attenuation protein (TRAP)-trp leader RNA interactions mediate translational as well as transcriptional regulation of the Bacillus subtilis trp operon. J. Bacteriol. 177, 6362–6370 (1995)

    CAS  Article  Google Scholar 

  7. 7

    Schilling, O., Langbein, I., Muller, M., Schmalisch, M. H. & Stulke, J. A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity. Nucleic Acids Res. 32, 2853–2864 (2004)

    CAS  Article  Google Scholar 

  8. 8

    Batey, R. T. Structures of regulatory elements in mRNAs. Curr. Opin. Struct. Biol. 16, 299–306 (2006)

    CAS  Article  Google Scholar 

  9. 9

    Cheah, M. T., Wachter, A., Sudarsan, N. & Breaker, R. R. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447, 497–500 (2007)

    CAS  ADS  Article  Google Scholar 

  10. 10

    Wachter, A. et al. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19, 3437–3450 (2007)

    CAS  Article  Google Scholar 

  11. 11

    Mazumder, B. et al. Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control. Cell 115, 187–198 (2003)

    CAS  Article  Google Scholar 

  12. 12

    Sampath, P. et al. Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation. Cell 119, 195–208 (2004)

    CAS  Article  Google Scholar 

  13. 13

    Braunstein, S. et al. A hypoxia-controlled cap-dependent to cap-independent translation switch in breast cancer. Mol. Cell 28, 501–512 (2007)

    CAS  Article  Google Scholar 

  14. 14

    Bastide, A. et al. An upstream open reading frame within an IRES controls expression of a specific VEGF-A isoform. Nucleic Acids Res. 36, 2434–2445 (2008)

    CAS  Article  Google Scholar 

  15. 15

    Ferrara, N. & Davis-Smyth, T. The biology of vascular endothelial growth factor. Endocr. Rev. 18, 4–25 (1997)

    CAS  Article  Google Scholar 

  16. 16

    Ray, P. S. & Fox, P. L. A post-transcriptional pathway represses monocyte VEGF-A expression and angiogenic activity. EMBO J. 26, 3360–3372 (2007)

    CAS  Article  Google Scholar 

  17. 17

    Mukhopadhyay, R. et al. DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression. Mol. Cell 32, 371–382 (2008)

    CAS  Article  Google Scholar 

  18. 18

    Liu, L. et al. Hypoxia-induced energy stress regulates mRNA translation and cell growth. Mol. Cell 21, 521–531 (2006)

    Article  Google Scholar 

  19. 19

    Sampath, P., Mazumder, B., Seshadri, V. & Fox, P. L. Transcript-selective translational silencing by gamma interferon is directed by a novel structural element in the ceruloplasmin mRNA 3′ untranslated region. Mol. Cell. Biol. 23, 1509–1519 (2003)

    CAS  Article  Google Scholar 

  20. 20

    Piñol-Roma, S., Swanson, M. S., Gall, J. G. & Dreyfuss, G. A novel heterogeneous nuclear RNP protein with a unique distribution on nascent transcripts. J. Cell Biol. 109, 2575–2587 (1989)

    Article  Google Scholar 

  21. 21

    Claffey, K. P. et al. Identification of a human VPF/VEGF 3′ untranslated region mediating hypoxia-induced mRNA stability. Mol. Biol. Cell 9, 469–481 (1998)

    CAS  Article  Google Scholar 

  22. 22

    Shih, S. C. & Claffey, K. P. Regulation of human vascular endothelial growth factor mRNA stability in hypoxia by heterogeneous nuclear ribonucleoprotein L. J. Biol. Chem. 274, 1359–1365 (1999)

    CAS  Article  Google Scholar 

  23. 23

    Jia, J., Arif, A., Ray, P. S. & Fox, P. L. WHEP domains direct noncanonical function of glutamyl-prolyl tRNA synthetase in translational control of gene expression. Mol. Cell 29, 679–690 (2008)

    CAS  Article  Google Scholar 

  24. 24

    Jaeger, J. A., Turner, D. H. & Zuker, M. Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA 86, 7706–7710 (1989)

    CAS  ADS  Article  Google Scholar 

  25. 25

    Knapp, G. Enzymatic approaches to probing RNA secondary and tertiary structure. Methods Enzymol. 180, 192–212 (1989)

    CAS  Article  Google Scholar 

  26. 26

    Brion, P. & Westhof, E. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26, 113–137 (1997)

    CAS  Article  Google Scholar 

  27. 27

    Huthoff, H. & Berkhout, B. Two alternating structures of the HIV-1 leader RNA. RNA 7, 143–157 (2001)

    CAS  Article  Google Scholar 

  28. 28

    Sudarsan, N. et al. Tandem riboswitch architectures exhibit complex gene control functions. Science 314, 300–304 (2006)

    CAS  ADS  Article  Google Scholar 

  29. 29

    Yaman, I. et al. The zipper model of translational control: a small upstream ORF is the switch that controls structural remodeling of an mRNA leader. Cell 113, 519–531 (2003)

    CAS  Article  Google Scholar 

  30. 30

    Merrick, W. C. & Hensold, J. O. Analysis of eukaryotic translation in purified and semipurified systems. Curr. Protocols. Cell Biol. Chapter 11, Unit–11.9 (2001)

    Google Scholar 

  31. 31

    Mazumder, B., Seshadri, V., Imataka, H., Sonenberg, N. & Fox, P. L. Translational silencing of ceruloplasmin requires the essential elements of mRNA circularization: Poly(A) tail, poly(A)-binding protein, and eukaryotic translation initiation factor 4G. Mol. Cell. Biol. 21, 6440–6449 (2001)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We are grateful to D. Driscoll and T. M. Henkin for helpful discussions. This work was supported by National Institutes of Health grants P01 HL29582, R01 HL67725 and P01 HL76491 (to P.L.F.), and R01 DK60596 (to M.H.).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Paul L. Fox.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-12 with Legends (PDF 1994 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ray, P., Jia, J., Yao, P. et al. A stress-responsive RNA switch regulates VEGFA expression. Nature 457, 915–919 (2009). https://doi.org/10.1038/nature07598

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.