Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein

EMBO Journal

Volumn 22, Issue 11, 2003, Pages 2821-2830

  Pérez Cañadillas, José Manuel ^a   Varani, Gabriele ^b  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Nuclear magnetic resonance; Polyadenylation; RNA processing; RNA recognition; RNA binding proteins

Indexed keywords

RNA BINDING PROTEIN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL MATURATION; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; MOLECULAR RECOGNITION; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA PROCESSING; TRANSACTIVATION;

AMINO ACID SEQUENCE; BASE COMPOSITION; BASE SEQUENCE; BINDING SITES; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

VERTEBRATA;

EID: 0037507248     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg259     Document Type: Article

References (49)

1. Allain, F.H.-T., Gubser, C.C., Howe, P.W.A., Nagai, K., Neuhaus, D. and Varani, G. (1996) Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature, 380, 646-650.
2. Allain, F.H.-T., Gilbert, D.E., Bouvet, P. and Feigon, J. (2000) Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target. J. Mol. Biol., 303, 227-241.
3. Avis, J., Allain, F.H.-T., Howe, P.W.A., Varani, G., Neuhaus, D. and Nagai, K. (1996) Solution structure of the N-terminal RNP domain of UIA protein: the role of C-terminal residues in structure stability and RNA binding. J. Mol. Biol., 257, 398-411.
4. Barabino, S.M.L. and Keller, W. (1999) Last but not least: regulated poly(A) tail formation. Cell, 99, 9-11.
5. Bard, J., Zhelkovsky, A.M., Helmling, S., Earnest, T.N., Moore, C.L. and Bohm, A. (2000) Structure of yeast poly(A) polymerase alone and in complex with 3′-dATP. Science, 289, 1346-1349.
6. Beaudoing, E., Freier, S., Wyatt, J.R., Claverie, J.M. and Gautheret, D. (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res., 10, 1001-1010.
7. Beyer, K., Dandekar, T. and Keller, W. (1997) RNA ligands selected by cleavage stimulation factor contain distinct sequence motifs that function as downstream elements in 3′-end processing of pre-mRNA. J. Biol. Chem., 272, 26769-26779.
8. Bienroth, S., Keller, W. and Wahle, E. (1993) Assembly of a processive polyadenylation complex. EMBO J., 12, 585-594.
9. Boelens, W.C., Jansen, E.J.R., van Venrooij, W.J., Stripecke, R., Mattaj, I.W. and Gunderson, S.I. (1993) The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA. Cell, 72, 881-892.
10. Calvo, O. and Manley, J.L. (2001) Evolutionarily conserved interaction between CtsF-64 and PC4 links transcription, polyadenylation and termination. Mol. Cell, 7, 1013-1023.
11. Chao, L., Jamil, A., Kim, S., Huang, L. and Martinson, H.G. (1999) Assembly of the cleavage and polyadenylation apparatus requires about 10 seconds in vivo and is faster for strong than for weak poly(A) sites. Mol. Cell. Biol., 19, 5588-5600.
12. Chen, C.-Y.A. and Shyu, A.-B. (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem. Sci., 20, 465-470.
13. Chuvpilo, S. et al. (1999) Alternative polyadenylation events contribute to the induction of NF-ATc in effector T cells. Immunity, 10, 261-269.
14. Colgan, D.F. and Manley, J.L. (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev., 11, 2755-2766.
15. Cornilescu, G., Delaglio, F. and Bax, A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR, 13, 289-302.
16. Dantonel, J.-C., Murthy, K.G.K., Manley J.L. and Tora, L. (1997) Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA. Nature, 389, 399-402.
17. Deo, R.C., Bonanno, J.B., Sonenberg, N. and Burley, S.K. (1999) Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell, 98, 835-845.
18. Ding, J., Hayashi, M.K., Zhang, Y., Manche, L., Krainer, A.R. and Xu, R.-M. (1999) Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev., 13, 1102-1115.
19. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol., 273, 283-298.
20. Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y. and Yokohama, S. (1999) Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature, 398, 579-585.
21. Hatton, L.S., Eloranta, J.J., Figureueiredo, L.M., Takagaki, Y., Manley, J.L. and O'Hare, K. (2000) The Drosophila homologue of the 64 kDa subunit of cleavage and stimulation factor interacts with the 77 kDa subunit encoded by the Suppressor of Forked gene. Nucleic Acids Res., 28, 520-526.
22. Howe, P.W.A., Nagai, K., Neuhaus, D. and Varani, G. (1994) NMR studies of U1 snRNA recognition by the N-terminal RNP domain of the human U1A protein. EMBO J., 13, 3873-3881.
23. Inoue, M., Muto, Y., Sakamoto, H. and Yokohama, S. (2000) NMR studies on functional structures of the AU-rich element-binding domains of Hu Antigen C. Nucleic Acids Res., 28, 1743-1750.
24. 65). EMBO J., 18, 4523-4534.
25. Kleiman, F.E. and Manley, J.L. (1999) Functional interaction of BRCA1-associated BARD1 with polyadenylation factor CstF-50. Science, 285, 1576-1579.
26. Kleiman, F.E. and Manley, J.L. (2001) The BARD1-CstF-50 interaction links mRNA 3′ end formation to DNA damage and tumor suppression. Cell. 104, 743-753.
27. Koradi, R., Billeter, M. and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph., 14, 51-55.
28. Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR, 8, 477-486.
29. Martin, G., Keller, W. and Doublié S. (2000) Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J., 19, 4193-4203.
30. Mittermaier, A., Varani, L., Muhandiram, D.R., Kay, L.E. and Varani, G. (1999) Changes in sidechain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein. J. Mol. Biol., 294, 967-979.
31. Nagai, K., Oubridge, C., Jessen, T.H., Li, J. and Evans, P.R. (1990) Structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature, 348, 515-520.
32. Nagata, T., Kurihara, Y., Matsuda, G., Saeki, J.-I., Kohno, T., Yanagida, Y., Ishikawa, F., Uesugi, S. and Katahira, M. (1999) Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0. J. Mol. Biol., 287, 221-237.
33. Price, S.R., Oubridge, C., Varani, G. and Nagai, K. (1998) Preparation of RNA-protein complexes for X-ray crystallography and NMR. In Smith, C. (ed.), RNA-Protein Interaction: A Practical Approach. Oxford University Press, Oxford, UK, pp. 37-74.
34. Proudfoot, N.J., Furger, A. and Dye, M.J. (2002) Integrating mRNA processing with transcription. Cell, 108, 501-512.
35. Sachs, A. and Varani, G. (2000) Eukaryotic translation initiation: there are (at least) two sides to every story. Nat. Struct. Biol., 7, 356-360.
36. Sattler. M., Schleucher, J. and Griesinger, C. (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. NMR Spectrosc., 34, 93-158.
37. Shamoo, Y., Krueger, U., Rice, L.M., Williams, K.R. and Steitz, T.A. (1997) Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 A resolution. Nat. Struct. Biol., 4, 215-222.
38. Shatkin, A.J. and Manley, J.L. (2000) The ends of the affair: capping and polyadenylation. Nat. Struct. Biol., 7, 838-842.
39. Takagaki, Y. and Manley, J.L. (1997) RNA recognition by the human polyadenylation factor CstF. Mol. Cell. Biol., 17, 3907-3914.
40. Takagaki, Y. and Manley, J.L. (1998) Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation. Mol. Cell, 2, 761-771.
41. Takagaki, Y. and Manley, J.L. (2000) Complex protein interactions within the human polyadenylation machinery identify a novel component. Mol. Cell. Biol., 20, 1515-1525.
42. Takagaki, Y., MacDonald, C.C., Shenk, T. and Manley, J.L. (1992) The human 64-kDa polyadenylation factor contains a ribonucleoprotein-type RNA binding domain and unusual auxiliary motifs. Proc. Natl Acad. Sci. USA, 89, 1403-1407.
43. Takagaki, Y., Seipelt, R.L., Peterson, M.L. and Manley, J.L. (1996) The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell, 87, 941-952.
44. Varani, G. and Nagai, K. (1998) RNA recognition by RNP proteins during RNA processing and maturation. Annu. Rev. Biophys. Biomol. Struct., 27, 407-445.
45. Varani, L., Gunderson, S., Kay, L.E., Neuhaus, D., Mattaj, I. and Varani, G. (2000) The NMR structure of the 38 kDa RNA-protein complex reveals the basis for cooperativity in inhibition of polyadenylation by human U1A protein. Nat. Struct. Biol., 7, 329-335.
46. Wahle, E. and Keller, W. (1996) The biochemistry of polyadenylation. Trends Biochem. Sci., 21, 247-250.
47. Wang, X. and Tanaka-Hall, T. (2001) Structural basis for recognition of AU-rich element RNA by Hu proteins. Nat. Struct. Biol., 8, 141-146.
48. Xu, R.-M., Jokhan, L., Cheng, X., Mayeda, A. and Krainer, A.R. (1997) Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure, 5, 559-570.
49. Zhao, J., Hyman, L. and Moore, C. (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation and interrelationship with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev., 63, 405-445.