Efficient detection of RNA-protein interactions using tethered RNAs

Nucleic Acids Research

Volumn 39, Issue 8, 2011, Pages

  Iioka, Hidekazu ^a,b   Loiselle, David ^c   Haystead, Timothy A ^c   MacAra, Ian G ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b KOBE UNIVERSITY   (Japan)

^c DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; FRAGILE X MENTAL RETARDATION PROTEIN; GREEN FLUORESCENT PROTEIN; PROTEIN CRUMBS3; RNA; STREPTAVIDIN; TRANSCRIPTION FACTOR; TRANSFER RNA; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; BINDING AFFINITY; BIOTINYLATION; CELL LYSATE; CONTROLLED STUDY; HUMAN; HUMAN CELL; INTRON; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN RNA BINDING; RNA SEQUENCE; RNA TRANSCRIPTION; RNA TRANSLATION;

APTAMERS, NUCLEOTIDE; CACO-2 CELLS; CHEMICAL PRECIPITATION; HEK293 CELLS; HUMANS; RNA, TRANSFER; RNA-BINDING PROTEINS;

EID: 79955630425     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1316     Document Type: Article

References (17)

1. Kawai, J., Shinagawa, A., Shibata, K., Yoshino, M., Itoh, M., Ishii, Y., Arakawa, T., Hara, A., Fukunishi, Y., Konno, H. et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature, 409, 685-690.
2. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature, 420, 563-573. (Pubitemid 35477049)
3. Birney, E., Stamatoyannopoulos, JA., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816. (Pubitemid 46920138)
4. Lecuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T.R., Tomancak, P. and Krause, H.M. (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell, 131, 174-187. (Pubitemid 47498530)
5. Prokipcak, R.D., Herrick, D J. and Ross, J. (1994) Purification and properties of a protein that binds to the C-terminal coding region of human c-myc mRNA. J. Biol. Chem., 269, 9261-9269. (Pubitemid 24209253)
6. Ross, A.F., Oleynikov, Y., Kislauskis, E.H., Taneja, K.L. and Singer, R.H. (1997) Characterization of a beta-actin mRNA zipcode-binding protein. Mol. Cell. Biol., 17, 2158-2165. (Pubitemid 27133302)
7. Mehta, A. and Driscoll, D.M. (1998) A sequence-specific RNA-binding protein complements apobec-1 to edit apolipoprotein B mRNA. Mol. Cell. Biol., 18, 4426-4432. (Pubitemid 28343027)
8. Said, N., Rieder, R., Hurwitz, R., Deckert, J., Urlaub, H. and Vogel, J. (2009) In vivo expression and purification of aptamer-tagged small RNA regulators. Nucleic Acids Res., 37, e133.
9. Zhou, Z. and Reed, R. (2003) Purification of functional RNA-protein complexes using MS2-MBP. Curr. Protoc. Mol. Biol., Chapter 27, Unit 27 23.
10. Windbichler, N. and Schroeder, R. (2006) Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer. Nat. Protoc., 1, 637-640.
11. Walker, S.C., Scott, F.H., Srisawat, C. and Engelke, D.R. (2008) RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. Methods Mol. Biol., 488, 23-40.
12. Hartmuth, K., Urlaub, H., Vornlocher, H.P., Will, C.L., Gentzel, M., Wilm, M. and Luhrmann, R. (2002) Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc Natl. Acad. Sci. USA, 99, 16719-16724. (Pubitemid 36034039)
13. Ponchon, L. and Dardel, F. (2007) Recombinant RNA technology: the tRNA scaffold. Nat. Methods, 4, 571-576. (Pubitemid 47214776)
14. Agris, P.F. (1996) The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. Prog. Nucleic Acid Res. Mol. Biol., 53, 79-129.
15. Srisawat, C. and Engelke, D.R. (2001) Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA, 7, 632-641. (Pubitemid 32416820)
16. Darnell, J.C., Jensen, K.B., Jin, P., Brown, V., Warren, S.T. and Darnell, R.B. (2001) Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell, 107, 489-499. (Pubitemid 33152784)
17. Li, Z., Wang, L., Hays, T.S. and Cai, Y. (2008) Dynein-mediated apical localization of crumbs transcripts is required for Crumbs activity in epithelial polarity. J. Cell. Biol., 180, 31-38.