Abstract
The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases and have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells.
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References
Niranjanakumari, S., Lasda, E., Brazas, R., and Garcia-Blanco, M. A. (2002) Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo, Methods 26, 182–190.
Hieronymus, H., and Silver, P. A. (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery, Nat Genet 33, 155–161.
Hurt, E., Luo, M. J., Rother, S., Reed, R., and Strasser, K. (2004) Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex, Proc Natl Acad Sci USA 101, 1858–1862.
Keene, J. D., Komisarow, J. M., and Friedersdorf, M. B. (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts, Nat Protoc 1, 302–307.
Tenenbaum, S. A., Lager, P. J., Carson, C. C., and Keene, J. D. (2002) Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays, Methods 26, 191–198.
Buratowski, S. (2009) Progression through the RNA polymerase II CTD cycle, Mol Cell 36, 541–546.
Conrad, N. K. (2008)Chapter 15. Co-immunoprecipitation techniques for assessing RNA-protein interactions in vivo, Methods Enzymol 449, 317–342.
Mili, S., and Steitz, J. A. (2004) Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses, RNA 10, 1692–1694.
Gilbert, C., Kristjuhan, A., Winkler, G. S., and Svejstrup, J. Q. (2004) Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation, Mol Cell 14, 457–464.
Selth, L. A., Gilbert, C., and Svejstrup, J. Q. (2009) RNA immunoprecipitation to determine RNA-protein associations in vivo, CSH Protoc 2009, pdb prot5234.
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Selth, L.A., Close, P., Svejstrup, J.Q. (2011). Studying RNA–Protein Interactions In Vivo By RNA Immunoprecipitation. In: Tollefsbol, T. (eds) Epigenetics Protocols. Methods in Molecular Biology, vol 791. Humana Press. https://doi.org/10.1007/978-1-61779-316-5_19
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DOI: https://doi.org/10.1007/978-1-61779-316-5_19
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