Molecular basis of FIR-mediated c-myc transcriptional control

Nature Structural and Molecular Biology

Volumn 17, Issue 9, 2010, Pages 1058-1064

  Cukier, Cyprian D ^a   Hollingworth, David ^a   Martin, Stephen R ^a   Kelly, Geoff ^b   Díaz Moreno, Irene ^a,c   Ramos, Andres ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b MEDICAL RESEARCH COUNCIL   (United Kingdom)

^c CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; FBP INTERACTING REPRESSOR PROTEIN; FUSE BINDING PROTEIN; NUCLEIC ACID BINDING PROTEIN; REPRESSOR PROTEIN; UNCLASSIFIED DRUG; DNA HELICASE; MYC PROTEIN; POLY-U BINDING SPLICING FACTOR 60KDA; RNA BINDING PROTEIN;

ARTICLE; DNA BINDING; GENE CONTROL; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; ONCOGENE C MYC; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PROTEIN DOMAIN; PROTEIN QUATERNARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DNA HELICASES; GENE EXPRESSION REGULATION; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, QUATERNARY; PROTO-ONCOGENE PROTEINS C-MYC; REPRESSOR PROTEINS; TRANSCRIPTION, GENETIC; RNA-BINDING PROTEINS;

EID: 77956339799     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1883     Document Type: Article

References (44)

1. Levens, D. Disentangling the MYC web. Proc. Natl. Acad. Sci. USA 99, 5757-5759 (2002).
2. Wierstra, I. & Alves, J. The c-myc promoter: still MysterY and challenge. Adv. Cancer Res. 99, 113-333 (2008).
3. Kenneth, N.S. & White, R.J. Regulation by c-Myc of ncRNA expression. Curr. Opin. Genet. Dev. 19, 38-43 (2009).
4. Meyer, N. & Penn, L.Z. Refecting on 25 years with MYC. Nat. Rev. Cancer 8, 976-990 (2008).
5. Kouzine, F., Liu, J., Sanford, S., Chung, H.J. & Levens, D. The dynamic response of upstream DNA to transcription-generated torsional stress. Nat. Struct. Mol. Biol. 11, 1092-1100 (2004).
6. Kouzine, F., Sanford, S., Elisha-Feil, Z. & Levens, D. The functional response of upstream DNA to dynamic supercoiling in vivo. Nat. Struct. Mol. Biol. 15, 146-154 (2008).
7. Liu, J. et al. Defective interplay of activators and repressors with TFIIH in xeroderma pigmentosum. Cell 104, 353-363 (2001).
8. Liu, J. et al. The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression. EMBO J. 25, 2119-2130 (2006).
9. Matsushita, K. et al. An essential role of alternative splicing of c-myc suppressor FUSE-binding protein-interacting repressor in carcinogenesis. Cancer Res. 66, 1409-1417 (2006).
10. Matsushita, K. et al. c-myc suppressor FBP-interacting repressor for cancer diagnosis and therapy. Front. Biosci. 14, 3401-3408 (2009).
11. Chung, H.J. et al. FBPs are calibrated molecular tools to adjust gene expression. Mol. Cell. Biol. 26, 6584-6597 (2006).
12. Benjamin, L.R. et al. Hierarchical mechanisms build the DNA-binding specifcity of FUSE binding protein. Proc. Natl. Acad. Sci. USA 105, 18296-18301 (2008).
13. Braddock, D.T., Louis, J.M., Baber, J.L., Levens, D. & Clore, G.M. Structure and dynamics of KH domains from FBP bound to single-stranded DNA. Nature 415, 1051-1056 (2002).
14. Davis-Smyth, T., Duncan, R.C., Zheng, T., Michelotti, G. & Levens, D. The far upstream element-binding proteins comprise an ancient family of single-strand DNA-binding transactivators. J. Biol. Chem. 271, 31679-31687 (1996).
15. Crichlow, G.V. et al. Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition. EMBO J. 27, 277-289 (2008).
16. Clery, A., Blatter, M. & Allain, F.H. RNA recognition motifs: boring? Not quite. Curr. Opin. Struct. Biol. 18, 290-298 (2008).
17. Beuth, B., Garcia-Mayoral, M.F., Taylor, I.A. & Ramos, A. Scaffold-independent analysis of RNA-protein interactions: the Nova-1 KH3-RNA complex. J. Am. Chem. Soc. 129, 10205-10210 (2007).
18. Hsiao, H.H. et al. Quantitative characterization of the interactions between c-myc transcriptional regulators FUSE, FBP and FIR. Biochemistry 49, 4620-4634 (2010).
19. Shamoo, Y., Abdul-Manan, N. & Williams, K.R. Multiple RNA binding domains (RBDs) just don't add up. Nucleic Acids Res. 23, 725-728 (1995).
20. Shamoo, Y. et al. Both RNA-binding domains in heterogenous nuclear ribonucleoprotein A1 contribute toward single-stranded-RNA binding. Biochemistry 33, 8272-8281 (1994).
21. Lunde, B.M., Moore, C. & Varani, G. RNA-binding proteins: modular design for effcient function. Nat. Rev. Mol. Cell Biol. 8, 479-490 (2007).
22. Rideau, A.P. et al. A peptide motif in Raver1 mediates splicing repression by interaction with the PTB RRM2 domain. Nat. Struct. Mol. Biol. 13, 839-848 (2006).
23. Lee, J.H., Rangarajan, E.S., Yogesha, S.D. & Izard, T. Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions. Structure 17, 833-842 (2009).
24. Soucek, L. et al. Modelling Myc inhibition as a cancer therapy. Nature 455, 679-683 (2008).
25. Bono, F. et al. Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex. EMBO Rep. 5, 304-310 (2004).
26. Kadlec, J., Izaurralde, E. & Cusack, S. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat. Struct. Mol. Biol. 11, 330-337 (2004).
27. Schellenberg, M.J. et al. Crystal structure of a core spliceosomal protein interface. Proc. Natl. Acad. Sci. USA 103, 1266-1271 (2006).
28. Lee, J.H., Rangarajan, E.S., Yogesha, S.D. & Izard, T. Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions. Structure 17, 833-842 (2009).
29. Kielkopf, C.L., Rodionova, N.A., Green, M.R. & Burley, S.K. A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell 106, 595-605 (2001).
30. Selenko, P. et al. Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol. Cell 11, 965-976 (2003).
31. Corsini, L. et al. U2AF-homology motif interactions are required for alternative splicing regulation by SPF45. Nat. Struct. Mol. Biol. 14, 620-629 (2007).
32. Price, S.R., Evans, P.R. & Nagai, K. Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394, 645-650 (1998).
33. Corsini, L. et al. Dimerization and protein binding specifcity of the U2AF homology motif of the splicing factor Puf60. J. Biol. Chem. 284, 630-639 (2009).
34. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55 (1996).
35. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).
36. Goddard, T.D. & Kneller, D.G. SPARKY 3. (University of California, San Francisco, 2004).
37. Linge, J.P., O'Donoghue, S.I. & Nilges, M. Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol. 339, 71-90 (2001).
38. Bartels, C., Xia, T.-h., Billeter, M., Güntert, P. & Wüthrich, K. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR 6, 1-10 (1995).
39. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289-302 (1999).
40. Brunger, A.T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 (1998).
41. Linge, J.P., Williams, M.A., Spronk, C.A., Bonvin, A.M. & Nilges, M. Refinement of protein structures in explicit solvent. Proteins 50, 496-506 (2003).
42. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486 (1996).
43. Schanda, P., Kupce, E. & Brutscher, B. SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J. Biomol. NMR 33, 199-211 (2005).
44. Kannt, A., Young, S. & Bendall, D.S. The role of acidic residues of plastocyanin in its interaction with cytochrome f. Biochim. Biophys. Acta 1277, 115-126 (1996).