A stress-responsive RNA switch regulates VEGFA expression (original) (raw)

• Mandal, M. & Breaker, R. R. Gene regulation by riboswitches. Nature Rev. Mol. Cell Biol. 5, 451–463 (2004)
  Article CAS Google Scholar
• Grundy, F. J. & Henkin, T. M. Regulation of gene expression by effectors that bind to RNA. Curr. Opin. Microbiol. 7, 126–131 (2004)
  Article CAS Google Scholar
• Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002)
  Article ADS CAS Google Scholar
• Cromie, M. J., Shi, Y., Latifi, T. & Groisman, E. A. An RNA sensor for intracellular Mg2+ . Cell 125, 71–84 (2006)
  Article CAS Google Scholar
• Grundy, F. J. & Henkin, T. M. tRNA as a positive regulator of transcription antitermination in B. subtilis . Cell 74, 475–482 (1993)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• Batey, R. T. Structures of regulatory elements in mRNAs. Curr. Opin. Struct. Biol. 16, 299–306 (2006)
  Article CAS Google Scholar
• 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)
  Article ADS CAS Google Scholar
• 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)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• Sampath, P. et al. Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation. Cell 119, 195–208 (2004)
  Article CAS Google Scholar
• Braunstein, S. et al. A hypoxia-controlled cap-dependent to cap-independent translation switch in breast cancer. Mol. Cell 28, 501–512 (2007)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• Ferrara, N. & Davis-Smyth, T. The biology of vascular endothelial growth factor. Endocr. Rev. 18, 4–25 (1997)
  Article CAS Google Scholar
• Ray, P. S. & Fox, P. L. A post-transcriptional pathway represses monocyte VEGF-A expression and angiogenic activity. EMBO J. 26, 3360–3372 (2007)
  Article CAS Google Scholar
• Mukhopadhyay, R. et al. DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression. Mol. Cell 32, 371–382 (2008)
  Article CAS Google Scholar
• Liu, L. et al. Hypoxia-induced energy stress regulates mRNA translation and cell growth. Mol. Cell 21, 521–531 (2006)
  Article Google Scholar
• 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)
  Article CAS Google Scholar
• 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
• 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)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• 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)
  Article CAS Google Scholar
• Jaeger, J. A., Turner, D. H. & Zuker, M. Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA 86, 7706–7710 (1989)
  Article ADS CAS Google Scholar
• Knapp, G. Enzymatic approaches to probing RNA secondary and tertiary structure. Methods Enzymol. 180, 192–212 (1989)
  Article CAS Google Scholar
• Brion, P. & Westhof, E. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26, 113–137 (1997)
  Article CAS Google Scholar
• Huthoff, H. & Berkhout, B. Two alternating structures of the HIV-1 leader RNA. RNA 7, 143–157 (2001)
  Article CAS Google Scholar
• Sudarsan, N. et al. Tandem riboswitch architectures exhibit complex gene control functions. Science 314, 300–304 (2006)
  Article ADS CAS Google Scholar
• 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)
  Article CAS Google Scholar
• 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
• 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)
  Article CAS Google Scholar