mRNPs take shape by CLIPPING and PAIRING

BioEssays

Volumn 28, Issue 11, 2006, Pages 1132-1143

  Denman, Robert B ^a  

^a NEW YORK STATE INSTITUTE FOR BASIC RESEARCH IN DEVELOPMENTAL DISABILITIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FRAGILE X MENTAL RETARDATION PROTEIN; MESSENGER RNA; RNA BINDING PROTEIN;

CELL METABOLISM; CHEMICAL MODIFICATION; CROSS LINKING; EXPRESSED SEQUENCE TAG; GEL MOBILITY SHIFT ASSAY; HUMAN; IMMUNOFLUORESCENCE MICROSCOPY; IMMUNOPRECIPITATION; IN VITRO STUDY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

ANIMALS; BIOCHEMISTRY; HUMANS; IMMUNOPRECIPITATION; PROTEIN BINDING; RNA, MESSENGER; RNA-BINDING PROTEINS;

EID: 33750840310     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20491     Document Type: Review

References (81)

1. Huang Y-S, Carson JH, Barbarese E, Richter JD. 2003. Facilitation of dendritic mRNA transport by CPEB. Genes Dev. 17(5):638-653.
2. Liu J, Hu J-Y, Wu F, Schwartz JH, Schacher S. 2006. Two mRNA-Binding Proteins Regulate the Distribution of Syntaxin mRNA in Aplysia Sensory Neurons. J Neurosci 26:5204-5214.
3. Cao X, Yeo G, Muotri AR, Kuwabara T, Gage FH. 2006. Noncoding RNAS in the mammalian central nervous system. Annual Review of Neuroscience 2977-103.
4. Goldstrohm AC, Hook BA, Seay DJ, Wickens M. 2006. PUF proteins bind Pop2p to regulate messenger RNAs. Nat Struct Mol Biol 13:533-539.
5. Antar LN, Afroz R, Dictenberg JB, Carroll RC, Bassell GJ. 2004. Metabotropic glutamate receptor activation regulates fragile X mental retardation protein and Fmr1 mRNA localization differentially in dendrites and at synapses. J Neurosci 24:2648-2655.
6. Antar LN, Dictenberg JB, Plociniak M, Afroz R, Bassell GJ. 2005. Localization of FMRP-associated mRNA granules and requirement of microtubules for activity-dependent trafficking in hippocampal neurons. Genes Brain Behavior 4:350-359.
7. Buckanovich RJ, Darnell RB. 1997. The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo. Mol Cell Biol 17:3194-3201.
8. Jensen K, Dredge B, Stefani G, Zhong R, Buckanovich R, et al. 2000. Nova-1 regulate neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25:359-371.
9. Serin G, Joseph G, Ghisolfi L, Bauzan M, Erard M, et al. 1997. Two RNA-binding domains determine the RNA-binding specificity of nucleolin. J Biol Chem 272:13109-13116.
10. Dreyfuss G, Matunis M, Pinol-Roma S, Burd C. 1993. hnRNP proteins and the biogenesis of mRNA. Ann Rev Biochem 62:289-321.
11. Martin KC, Zukin RS. 2006. RNA trafficking and local protein synthesis in dendrites: an overview. J Neurosci 26:7131-7134.
12. Wells DG. 2006. RNA-binding proteins: a lesson in repression. J Neurosci 267135-7138.
13. Hirokawa N. 2006. mRNA transport in dendrites: RNA granules, motors, and tracks. J Neurosci 26:7139-7142.
14. Schuman EM, Dynes JL, Steward O. 2006. Synaptic regulation of translation of dendritic mRNAs. J Neurosci 26:7143-7146.
15. Pfeiffer BE, Huber KM. 2006. Current advances in local protein synthesis and synaptic plasticity. J Neurosci 26:7147-7150.
16. Grossman AW, Aldridge GM, Weiler IJ, Greenough WT. 2006. Local protein synthesis and spine morphogenesis: fragile X syndrome and beyond. J Neurosci 26:7151-7155.
17. Keene JD. 2001. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. PNAS 98:7018-7024.
18. Keene J, Tenenbaum S. 2002. Eucaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9:1161-1167.
19. Musco G, Kharrat A, Stier G, Faternali F, Gibson TJ, et al. 1997. The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome [letter] [published erratum appears in Nat Struct Biol 1997 Oct;4(10):840]. Nat Struct Biol 4:712-716.
20. Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, et al. 1996. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Cell 85:237-245.
21. Castiglone Morelli MA, Stier G, Gibson T, Joseph C, Musco G, et al. 1995. The KH module has an alpha beta fold. FEBS Lett 358:193-198.
22. Siomi H, Choi M, Siomi MC, Nussbaum RL, Dreyfuss G. 1994. Essential role for KH domains in RNA binding: impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome. Cell 77:33-39.
23. Davidovic L, Bechara E, Gravel M, Jaglin XH, Tremblay S, et al. 2006. The nuclear microSpherule protein 58 is a novel RNA-binding protein that interacts with fragile X mental retardation protein in polyribosomal mRNPs from neurons. Hum Mol Genet 15:1525-1538.
24. Thisted T, Lyakhov DL, Liebhaber SA. 2001. Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and alpha CP-2KL. suggest distinct modes of RNA recognition. J Biol Chem 276:17484-17496.
25. Zhang YQ, Bailey AM, Matthies HJ, Renden RB, Smith MA, et al. 2001. Drosophila fragile X-related gene regulates the MAP1B homolog futsch to control synaptic structure and function. Cell 107:591-603.
26. De Diego Otero Y, Severijnen L-A, van Cappellen G, Schrier M, Oostra B, et al. 2002. Transport of fragile X mental retardation protein via granules in neurites of PC12 Cells. Mol Cell Biol 22:8332-8341.
27. SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S, et al. 1996. A three-hybrid system to detect RNA-protem interactions in vivo. Proc Natl Acad Sci USA 93:8496-8501.
28. Siomi H, Siomi MC, Nussbaum RL, Dreyfuss G. 1993. The protein product of the fragile X gene, FMR1, has characteristics of an RNA-binding protein. Cell 74:291-298.
29. Brown V, Small K, Lakkis L, Feng Y, Gunter C, et al. 1998. Purified recombinant Fmrp exhibits selective RNA binding as an intrinsic property of the fragile X mental retardation protein. J Biol Chem 273:15521-15527
30. Sung Y-J, Conti J, Currie JR, Brown WT, Denman RB. 2000. RNAs that interact with the fragile X syndrome RNA binding protein FMRP. Biochem Biophys Res Commun 275:973-980.
31. Darneli JC, Jensen KB, Jin P, Brown V, Warren ST, et al. 2001. Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell 107:489-499.
32. Schaeffer C, Bardoni B, Mandel J-L, Ehresmann B, Ehresmann C, et al. 2001. The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif. EMBO J 20:4803-4813.
33. Chen L, Yun S-W, Seto J, Liu W, Toth M. 2003. The fragile x mental retardation protein binds and regulates a novel class of mRNAs containing a rich target sequences. Neuroscience 120:1005-1017.
34. Brown V, Jin P, Ceman S, Darneli JC, O'Donnell WT, et al. 2001. Microarray identification of FMRP-associaled brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107:477-487.
35. Dolzhanskaya N, Sung YJ, Conti J, Currie JR, Denman RB. 2003. The fragile X mental retardation protein interacts with U-rich RNAs in a yeast three-hybrid system. Biochemical and Biophysical Research Communications 305:434-441.
36. Sung Y-J, Dolzhanskaya N, Nlin SL, Brown WT, Currie JR, et al. 2003. The fragile X mental retardation protein FMRP binds elongation factor 1A mRNA and negatively regulates its translation in vivo. J Biol Chem 278:15669-15678.
37. Ashley CT Jr, Wilkinson KD, Reines D, Warren ST. 1993. FMR1 protein: conserved RNP family domains and selective RNA binding, Science 262:563-566
38. Li Z, Zhang Y, Ku L, Wilkinson KD, Warren ST, et al. 2001. The fragile X mental retardation protein inhibits translation via interacting with mRNA. Nucleic Acids Res 29:2276-2283.
39. Miyashiro KY, Beckel-Mitchener A, Purk TP, Becker KG, Barret T, et al. 2003. RNA cargoes associating with FMRP reveal deficits in cellular functioning in Fmr1 null mice. Neuron 37:417-431.
40. Ule J, Jensen K, Ruggiu AM, Ule A, Darneli R. 2003. CLIP identifies Nova-regulated RNA networks in the brain. Science 302:1212-1215.
41. Rackham O, Brown CE. 2004. Visualization of RNA-Protein interactions in living cells: FMRP and IMP1 interact on mRNAs. EMBO J 23:3346-3355.
42. Zielinski J, Kilk K, Peritz T, Kannanayakal T, Miyashiro KY, et al. 2006. In vivo identification of ribonucleoprotein-RNA interactions. PNAS 103:1557-1562.
43. Pestova T, Shatsky I, Hellen CUT. 1996. Functional dissection of eucaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S pre-initiation complexes. Molecular and Cellular Biology 166870-6878.
44. Wang W, Krug RM. 1998. U6atac snRNA, the highly divergent counter-part of U6 snRNA, is the specific target that mediates inhibition of AT-AC splicing by the influenza virus NS1 protein. RNA 4:55-64.
45. Kolupaeva VG, Lomakin I, Pestova T, Hellen CUT. 2003. Eucaryotic initiation factors 4G and 4A mediate conformational changes down-stream of the initiation codon of the Encephalomyocarditis virus internal ribosome entry site. Molecular and Cellular Biology 23:687-698.
46. Nurse K, Colgan J, Denman R, Wilhelm J, Ofengand J. 1987. Covalent cross-linking of AcVal-tRNA to Tetrahymena thermophila cytoplasmic ribosomes and two of its 17S rRNA mutants. Biochimie 69:1105-1112.
47. Denman R, Colgan J, Nurse K, Ofengand J. 1988. Crosslinking of the anticodon of P site bound tRNA to C-1400 of E.coli 16S RNA does not require the participation of the 50S subunit. Nucleic Acids Res 16:165-178.
48. Urlaub H, Hartmuth K, Kostka S, Grelle G, Luhrmann R. 2000. A general approach for identification of RNA-protein crosslinking sites within native human spliceosomal small nuclear ribonucleoproteins (snRNPs). J Biol Chem 275:41458-41468.
49. Wozniak AK, Nottrott S, Kuhn-Holsken EVA, Schroder GF, Grubmuller H. et al. 2005. Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements. RNA 11:1545-1554.
50. Sung Y-J, Denman RB. 2001. RNA binding properties of the fragile X syndrome mental retardation protein FMRP. Recent Res Devel Biophys Biochem 1:109-123.
51. Darnell JC, Fraser CE, Mostovetsky O, Stefani G, Jones TA, et al. 2005. Kissing complex RNAs mediate interaction between the fragile-X mental retardation protein KH2 domain and brain polyribosomes. Genes Dev 19:903-918.
52. Letters H, Dejgaard K, Celis JE. Characterisation of two major cellular poly(rC)-binding human proteins, each containing three K-homologous (KH) domains. 1995. Eur J Biochem 230:447-453.
53. Mears WE, Rice SA. 1996. The RGG box motif of the herpes simplex virus ICP27 protein mediates an RNA-binding activity and determines in vivo methylation. J Virol 70:7445-7453.
54. Wang H, Iacoangeli A, Lin D, Williams K, Denman RB, et al. 2005. Dendritic BC1 RNA in translational control mechanisms. J Cell Biol 171:811-821.
55. Wang H, Iacoangeli A, Popp S, Muslimov I, Imataka H, et al. 2003. Dendritic BC1 RNA: functional role in regulation of translational initiation. J Neurosci 22:10232-10241.
56. Jayasena VK, Gold L. 1997. In vitro selection of self-cleaving RNAs with a low pH optimum. Proc Natl Acad Sci USA 94:10612-10617.
57. Darnell JC, Warren ST, Darnell RB. 2004. The fragile X mental retardation protein, FMRP, recognizes G-quartets. Ment Retard Dev Disabil Res Rev 10:49-52.
58. Schaeffer C, Didiot M-C, Tian Z, Ehresmann B, Ehresmann C, et al. 2005. FMRP and the G-quartets. In: Sung YJ, Denman RB, editors. The Molecular Basis of Fragile X Syndrome. Trivandrum: Research Signpost; p 51-64.
59. Dolzhanskaya N, Merz G, Aletta JM, Denman RB. 2006. Methylation regulates FMRP's intracellular protein-protein and protein-RNA interactions. J Cell Sci 119:1933-1946.
60. Stetler A, Winograd C, Sayegh J, Cheever A, Patton E, et al. 2006. Identification and characterization of the methyl arginines in the fragile X mental retardation protein Fmrp. Hum Mol Gen 15:87-96.
61. Price DK, Zhang F, Ashley CT Jr, Warren ST. 1996. The chicken FMR1 gene is highly conserved with a CCT 5′-untranslated repeat and encodes an RNA-binding protein. Genomics 31:3-12.
62. Gabus C, Mazroui R, Tremblay S, Khandjian EW, Darlix J-L. 2004. The fragile X mental retardation protein has nucleic acid chaperone properties. Nucl Acids Res 32:2129-2137.
63. Bernstein DS, Buter N, Stumpf C, Wickens M. 2002. Analyzing mRNA-protein complexes using a yeast three-hybrid system. Methods 26:123-141.
64. Hook B, Bernstein D, Zhang B, Wickens M. 2005. RNA-protein interactions in the yeast three-hybrid system: Affinity, sensitivity, and enhanced library screening. RNA 11:227-233.
65. Kuhn-Holsken EVA, Lenz C, Sander B, Luhrmann R, Urlaub H. 2005. Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles. RNA 11:1915-1930.
66. Rhode BM, Hartmuth K, Urlaub H, Luhrmann R. 2003. Analysis of site-specific protein-RNA cross-links in isolated RNP complexes, combining affinity selection and mass spectrometry. RNA 9:1542-1551.
67. Urlaub H, Hartmuth K, Kostka S, Grelle G, Luhrmann R. 2000. A General Approach for Identification of RNA-Protein Cross-linking Sites within Native Human Spliceosomal Small Nuclear Ribonucleoproteins (snRNPs). Analysis of RNA-protein contacts in native U1 and U4/U6.U5 snRNPs. J Biol Chem 275:41458-41468.
68. Ule J, Jensen K, Mele A, Darnell RB. 2005. CLIP: A method for identifying protein-RNA interaction sites in living cells. Methods 37:376-386.
69. Palacios IM, St. Johnston D. 2002. Kinesin light chain-dependent function of the kinesin heavy chain in cytoplasmic streaming and posterior localisation in the Drosophila oocyte. Development 129:5473-5485.
70. Irwin N, Baekelandt V, Goritchenko L, Benowitz LI. 1997. Identification of two proteins that bind to a pyrimidine-rich sequence in the 3′-untranslated region of GAP-43 mRNA. Nucl Acids Res 25:1281-1288.
71. Chung S, Jiang L, Cheng S, Furneaux H. 1996. Purification and properties of HuD, a neuronal RNA-binding protein. J Biol Chem 271:11518-11524.
72. Hayman ML, Read LK. 1999. Trypanosoma brucei RBP16 Is a Mitochondrial Y-box Family Protein with Guide RNA Binding Activity. J Biol Chem 274:12067-12074.
73. Smith CA, Calabro V, Frankel AD. 2000. An RNA-binding chameleon. Mol Cell 6:1067-1076.
74. Bertrandy S, Burlet P, Clermont O, Huber C, Fondrat C, et al. 1999. The RNA-binding properties of SMN: deletion analysis of the zebrafish orthologue defines domains conserved in evolution. Hum Mol Gen 8:775-782.
75. Johnstone BH, Handler AA, Chao DK, Nguyen V, Smith M, et al. 1999. The widely conserved Era G-protein contains an RNA-binding domain required for Era function in vivo. Mol Microbiol 33:1118-1131.
76. Zorn AM, Krieg PA. 1997. The KH domain protein encoded by quaking functions as a dimer and is essential for notochord development in Xenopus embryos. Genes Dev 11:2176-2190.
77. Saffman EE, Styhler S, Rother K, Li W, Richard S, et al. 1998. Premature translation of oskar in oocytes lacking the RNA-binding protein bicaudal-C. Mol Cell Biol 18:4855-4862.
78. Zhang S, Grosse F. 1997. Domain structure of human nuclear DNA helicase II (RNA helicase A). J Biol Chem 272:11487-11494.
79. Arning S, Gruter P, Silbe G, Kramer A. 1996. Mammalian splicing factor SF1 is encoded by variant cDNAs and binds to RNA. RNA 2:794-810.
80. Ostrowski J, Kawata Y, Schullery DS, Denisenko ON, Higaki Y, et al. 2001. Insulin alters heterogeneous nuclear ribonucleoprotein K protein binding to DNA and RNA. PNAS 98:9044-9049.
81. Siomi MC, Siomi H, Sauer WH, Srinivasan S, Nussbaum RL, et al. 1995. FXR1, an autosomal homolog of the fragile X mental retardation gene. EMBO J 14:2401-2408.