Abstract
Argonaute proteins are key factors in RNA silencing. After association with small RNAs of 20–30 Ânucleotides, Argonaute proteins are targeted to homologous RNA molecules that are to be silenced. To understand the functional contributions of Argonaute proteins to RNA silencing at a biochemical level, immunoisolation of Argonaute proteins from living cells of various organisms has been performed. This has enabled the analysis of Argonaute-associated proteins and RNAs. Identifying the small RNAs that associate with individual Argonaute proteins, for instance, could help to elucidate the silencing pathways in which particular Argonaute proteins are involved. However, it is also necessary to note that the results obtained through such biochemical analyzes are greatly affected by the quality and properties of the antibodies used, as well as by the immunoprecipitation conditions employed, including buffer contents and/or salt concentration. In this chapter, we describe fundamental methods for immunoprecipitating Argonaute proteins using monoclonal antibodies as well as for detecting associated proteins and small RNAs. Furthermore, we will also explain how various parameters, such as antibody properties and buffer conditions, can alter the production and interpretation of experimental data.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Siomi, H., and Siomi, M. C. (2009). On the road to reading the RNA-interference code. Nature 457, 396–404.
Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233.
Malone, C. D., and Hannon, G. J. (2009). Small RNAs as guardians of the genome. Cell 136, 656–668.
Voinnet, O. (2009). Origin, biogenesis, and activity of plant microRNAs. Cell 136, 669–687.
Hutvagner, G., and Simard, M. J. (2008). Argonaute proteins: key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 9, 22–32.
Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., and Joshua-Tor, L. (2003). The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10, 1026–1032.
Ma, J. B., Ye, K., and Patel, D. J. (2004). Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318–22.
Lingel, A., Simon, B., Izaurralde, E., and Sattler, M. (2004). Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nat. Struct. Mol. Biol. 11, 576–577.
Song, J. J., Smith, S. K., Hannon, G. J., and Joshua-Tor, L. (2004). Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434–1437.
Parker, J. S., Roe, S. M., and Barford, D. (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 23, 4727–4737.
Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson, J. M., Song, J. J., Hammond, S. M., Joshua-Tor, L., and Hannon, G. J. (2004). Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437–1441.
Farazi, T. A., Juranek, S. A., and Tuschl, T. (2008). The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135, 1201–1214.
Okamura, K., Ishizuka, A., Siomi, H., and Siomi, M. C. (2004). Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 18, 1655–1666.
Förstemann, K., Horwich, M. D., Wee, L., Tomari, Y., and Zamore, P. D. (2007). Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130, 287–297.
Miyoshi, K., Tsukumo, H., Nagami, T., Siomi, H., and Siomi, M. C. (2005). Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev. 19, 2837–2848.
Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F., and Hannon, G. J. (2004). Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235.
Saito, K., Ishizuka, A., Siomi, H., and Siomi, M. C. (2005). Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells. PLoS Biol. 3, e235.
Förstemann, K., Tomari, Y., Du, T., Vagin, V. V., Denli, A. M., Bratu, D. P., Klattenhoff, C., Theurkauf, W. E., and Zamore, P. D. (2005). Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3, e236.
Liu, Q., Rand, T. A., Kalidas, S., Du, F., Kim, H. E., Smith, D. P., and Wang, X. (2003). R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925.
Kim, V. N., Han, J., and Siomi, M. C. (2009). Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10, 126–139.
Zhou, R., Czech, B., Brennecke, J., Sachidanandam, R., Wohlschlegel, J. A., Perrimon, N., and Hannon, G. J. (2009). Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA 15, 1886–1895.
Hartig, J. V., Esslinger, S., Böttcher, R., Saito, K., and Förstemann, K. (2009). Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences. EMBO J. 28, 2932–2944.
Miyoshi, K., Miyoshi, T., Hartig, J. V., Siomi, H., and Siomi, M. C. (2010). Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and micro RNA biogenesis pathways in Drosophila. RNA, 16, 506–515.
Tolia, N. H., and Joshua-Tor, L. (2007). Slicer and the argonautes. Nat. Chem. Biol. 3, 36–43.
Saito, K., Sakaguchi, Y., Suzuki, T., Suzuki, T., Siomi, H., and Siomi, M.C. (2007). Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends. Genes Dev., 21, 1603–1608.
Kawamura, Y., Saito, K., Kin, T., Ono, Y., Asai, K., Sunohara, T., Okada, T. N., Siomi, M. C., and Siomi, H. (2008). Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453, 793–797.
Pall, G. S., and Hamilton, A. J. (2008). Improved northern blot method for enhanced detection of small RNA. Nat. Protoc. 3, 1077–1084.
Acknowledgments
We thank Asuka Azuma-Mukai for technical assistance and other members of the Siomi laboratory for comments and for critical reading of the manuscript. This work was supported by Mochida Memorial Foundation for Medical and Pharmaceutical Research grants to K.M., MEXT grants to H.S. and NEDO (New Energy and Industrial Technology Development Organization) grants to M.C.S. M.C.S. is supported by CREST from JST.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Miyoshi, K., Okada, T.N., Siomi, H., Siomi, M.C. (2011). Biochemical Analyzes of Endogenous Argonaute Complexes Immunopurified with Anti-Argonaute Monoclonal Antibodies. In: Hobman, T., Duchaine, T. (eds) Argonaute Proteins. Methods in Molecular Biology, vol 725. Humana Press. https://doi.org/10.1007/978-1-61779-046-1_3
Download citation
DOI: https://doi.org/10.1007/978-1-61779-046-1_3
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-045-4
Online ISBN: 978-1-61779-046-1
eBook Packages: Springer Protocols