Résumés
Résumé
Les interactions ARN-protéines interviennent dans de nombreuses fonctions. Ces interactions se font le plus souvent au sein d’assemblages macromoléculaires complexes. Des développements méthodologiques récents ont permis des avancées importantes dans la compréhension de la spécificité de ces interactions. L’objectif de cet article est d’exposer les différentes techniques d’étude des complexes ARN-protéines ainsi que les dernières données concernant l’utilisation thérapeutique des ARN.
Summary
RNA-proteins interactions are involved in numerous cellular functions. These interactions are found in most cases within complex macromolecular assemblies. The recent development of tools and techniques to study RNA-protein complexes has significantly increased our knowledge in the nature of these specific interactions. The aim of this article is to present the different techniques used to study RNA-protein complexes, as well as recent data concerning the application of RNA as therapeutic molecules.
Parties annexes
Références
- 1. Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism.Nucleic Acids Res 2002; 30: 1427-64.
- 2. Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.Science 1990; 249: 505-10.
- 3. Singer BS, Shtatland T, Brown D, Gold L. Libraries for genomic SELEX.Nucleic Acids Res 1997; 25: 781-6.
- 4. Stelzl U, Nierhaus KH. SERF: in vitro election of random RNA fragments to identify protein binding sites within large RNAs.Methods 2001; 25: 351-7.
- 5. Drolet DW, Jenison RD, Smith DE, Pratt D, Hicke BJ. A high throughput platform for systematic evolution of ligands by exponential enrichment (SELEX).Comb ChemHigh Throughput Screen 1999; 2: 271-8.
- 6. Ghisolfi-Nieto L, Joseph G, Puvion-Dutilleul F, Amalric F, Bouvet P. Nucleolin is a sequence-specific RNA-binding protein: characterization of targets on pre-ribosomal RNA.J Mol Biol 1996; 260: 34-53.
- 7. Serin G, Joseph G, Faucher C, et al. Localization of nucleolin binding sites on human and mouse pre-ribosomal RNA.Biochimie 1996; 78: 530-8.
- 8. Ginisty H, Serin G, Ghisolfi-Nieto L, et al. Interaction of nucleolin with an evolutionarily conserved pre-ribosomal RNA sequence is required for the assembly of the primary processing complex.J Biol Chem 2000; 275: 18845-50.
- 9. Tsai DE, Harper DS, Keene JD. U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts.Nucleic Acids Res 1991; 19: 4931-6.
- 10. Katsamba PS, Park S, Laird-Offringa IA. Kinetic studies of RNA-protein interactions using surface plasmon resonance.Methods 2002; 26: 95-104.
- 11. Darnell JC, Jensen KB, Jin P, Brown V, Warren ST, Darnell RB. Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function.Cell 2001; 107: 489-99.
- 12. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays.Methods 2002; 26: 191-8.
- 13. Brown V, Jin P, Ceman S, et al. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome.Cell 2001; 107: 477-87.
- 14. Schaeffer C, Bardoni B, Mandel JL, Ehresmann B, Ehresmann C, Moine H. The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif.Embo J 2001; 20: 4803-13.
- 15. Rodgers ND, Jiao X, Kiledjian M. Identifying mRNAs bound by RNA-binding proteins using affinity purification and differential display.Methods 2002; 26: 115-22.
- 16. Bachler M, Schroeder R, von Ahsen U. StreptoTag: a novel method for the isolation of RNA-binding proteins.Rna 1999; 5: 1509-16.
- 17. Paillard L, Omilli F, Legagneux V, Bassez T, Maniey D, Osborne HB. EDEN and EDEN-BP, a cis element and an associated factor that mediate sequence-specific mRNA deadenylation in Xenopus embryos.Embo J 1998; 17: 278-87.
- 18. SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S, Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo.Proc Natl Acad Sci USA 1996; 93: 8496-501.
- 19. Martin F, Schaller A, Eglite S, Schumperli D, Muller B. The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein.Embo J 1997; 16: 769-78.
- 20. Sagesser R, Martinez E, Tsagris M, Tabler M. Detection and isolation of RNA-binding proteins by RNA-ligand screening of a cDNA expression library.Nucleic Acids Res 1997; 25: 3816-22.
- 21. Harada K, Martin SS, Frankel AD. Selection of RNA-binding peptides in vivo.Nature 1996; 380: 175-9.
- 22. Jain C, Belasco JG. A structural model for the HIV-1 Rev-RRE complex deduced from altered- specificity rev variants isolated by a rapid genetic strategy.Cell 1996; 87: 115-25.
- 23. Bouvet P, Jain C, Belasco JG, Amalric F, Erard M. RNA recognition by the joint action of two nucleolin RNA-binding domains: genetic analysis and structural modeling.Embo J 1997; 16: 5235-46.
- 24. Danner S, Belasco JG. T7 phage display: a novel genetic selection system for cloning RNA-binding proteins from cDNA libraries.Proc Natl Acad Sci USA 2001; 98: 12954-9.
- 25. Andersen JS, Lyon CE, Fox AH, et al. Directed proteomic analysis of the human nucleolus.Curr Biol 2002; 12:1-11.
- 26. Scherl A, Coute Y, Deon C, et al. Functional proteomic analysis of human nucleolus.Mol Biol Cell 2002; 13: 4100-9.
- 27. Dragon F, Gallagher JE, Compagnone-Post PA, et al. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.Nature 2002; 417: 967-70.
- 28. Honey S, Schneider BL, Schieltz DM, Yates JR, Futcher B. A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-CDK complex.Nucleic Acids Res 2001; 29: E24.
- 29. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration.Nat Biotechnol 1999; 17: 1030-2.
- 30. Mendell JT, Dietz HC. When the message goes awry: disease-producing mutations that influence mRNA content and performance.Cell 2001; 107: 411-4.
- 31. Charlet BN, Savkur RS, Singh G, Philips AV, Grice EA, Cooper TA. Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing. Mol Cell 2002; 10:45-53.
- 32. Xavier KA, Eder PS, Giordano T. RNA as a drug target: methods for biophysical characterization and screening.Trends Biotechnol 2000; 18: 349-56.
- 33. Schlunzen F, Zarivach R, Harms J, et al. A. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.Nature 2001; 413: 814-21.
- 34. Opalinska JB, Gewirtz AM. Nucleic-acid therapeutics: basic principles and recent applications.Nat Rev Drug Discov 2002; 1: 503-14.
- 35. Sullenger BA, Gilboa E. Emerging clinical applications of RNA.Nature 2002; 418: 252-8.
- 36. Tanabe T, Kuwabara T, Warashina M, Tani K. Taira K, Asano S. Oncogene inactivation in a mouse model.Nature 2000; 406: 473-4.
- 37. Sullenger BA, Gallardo HF, Ungers GE, Gilboa E. Overexpression of TAR sequences renders cells resistant to human immunodeficiency virus replication.Cell 1990; 63: 601-8.
- 38. Darfeuille F, Arzumanov A, Gryaznov S, Gait MJ, Di Primo C, Toulme JJ. Loop-loop interaction of HIV-1 TAR RNA with N3’—>P5’ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription.Proc Natl Acad Sci USA 2002; 99: 9709-14.
- 39. Ulrich H, Magdesian MH, Alves MJ, Colli W. In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion.J Biol Chem 2002; 277: 20756-62.
- 40. Drolet DW, Nelson J, Tucker CE, et al. Pharmacokinetics and safety of an anti-vascular endothelial growth factor aptamer (NX1838) following injection into the vitreous humor of Rhesus monkeys.Pharm Res 2000; 17: 1503-10.
- 41. Rusconi CP, Scardino E, Layzer J, et al. RNA aptamers as reversible antagonists of coagulation factor IXa.Nature 2002; 419: 90-4.
- 42. Lawrence D. RNAi could hold promise in the treatment of HIV.Lancet 2002; 359: 2007.
- 43. Birney ES, Kumar S, Krainer AR. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res 1993; 21: 5803-16.
- 44. Allain FH, Gilbert DE, Bouvet P, Feigon J. 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 2000; 303: 227-41.
- 45. Ginisty H, Amalric F, Bouvet P. Two different combinations of RNA-binding domains determine the RNA binding specificity of nucleolin. J Biol Chem 2001; 276: 14338-43.
- 46. De Boulle K, Verkerk AJ, Reyniers E, et al. A point mutation in the FMR-1 gene associated with fragile X mental retardation. Nat Genet 1993; 3:31-5.
- 47. Darnell JC, Jensen KB, Jin P, Brown V, Warren ST, Darnell RB. Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell 2001; 107: 489-99.
- 48. Schaeffer C, Bardoni B, Mandel JL, Ehresmann B, Ehresmann C, Moine H. The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif. EMBO J 2001; 20: 4803-13.
- 49. Ghisolfi L, Joseph G, Amalric F, Erard M. The glycine-rich domain of nucleolin has an unusual supersecondary structure responsible for its RNA-helix-destabilizing properties. J Biol Chem 1992; 267: 2955-9.
- 50. Birney E, Kumar S, Krainer AR. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res 1993; 21: 5803-16.
- 51. Bouvet P, Diaz JJ, KindbeiterK, Madjar JJ, Amalric F. Nucleolin interacts with several ribosomal proteins through its RGG domain. J Biol Chem 1998; 273: 19025-9.
- 52. Hanakahi LA, Sun H, Maizels N. High affinity interactions of nucleolin with G-G-paired rDNA. J Biol Chem 1999; 274: 15908-12.
- 53. Ryter JM, Schultz SC. Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA. EMBO J 1998; 17: 7505-13.
- 54. Ramos A, Grunert S, AdamsJ, et al. RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J 2000; 19: 997-1009.
- 55. Conrad C, Rauhut R. Ribonuclease III: new sense from nuisance. Int J Biochem Cell Biol 2002; 34: 116-29.
- 56. Tan R, Frankel AD. Structural variety of arginine-rich RNA-binding peptides. Proc Natl Acad Sci USA 1995; 92: 5282-6.
- 57. Weiss MA, Narayana N. RNA recognition by arginine-rich peptide motifs. Biopolymers 1998; 48: 167-80.
- 58. Campisi DM, Calabro V, Frankel AD. Structure-based design of a dimeric RNA-peptide complex. EMBO J 2001; 20: 178-86.