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Genome-Wide Analysis of RNA-Protein Interactions in Plants

  • Alice Barkan
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 553)

Abstract

RNA–protein interactions profoundly impact organismal development and function through their contributions to the basal gene expression machineries and their regulation of post-transcriptional processes. The repertoire of predicted RNA binding proteins (RBPs) in plants is particularly large, suggesting that the RNA–protein interactome in plants may be more complex and dynamic even than that in metazoa. To dissect RNA–protein interaction networks, it is necessary to identify the RNAs with which each RBP interacts and to determine how those interactions influence RNA fate and downstream processes. Identification of the native RNA ligands of RBPs remains a challenge, but several high-throughput methods for the analysis of RNAs that copurify with specific RBPs from cell extract have been reported recently. This chapter reviews approaches for defining the native RNA ligands of RBPs on a genome-wide scale and provides a protocol for a method that has been used to this end for RBPs that localize to the chloroplast.

Key words

RNA–protein interaction RIP-chip RNA coimmunoprecipitation microarray RNA binding protein 

Notes

Acknowledgments

I would like to thank Rosalind Williams-Carrier and Christian Schmitz-Linneweber for their central contributions in developing our RIP-chip methodology, Eric Johnson and his laboratory for guidance in microarray printing and hybridization, and Jana Prikryl, Yukari Asakura, Susan Belcher, and Kenneth Watkins for optimizing aspects of the protocols. I would also like to thank Rodger Voelker, Todd Mockler, and Don Rio for stimulating discussions and for their comments on the manuscript and Don Rio for communicating results prior to publication. This work was supported by grant DBI-0421799 from the National Science Foundation.

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Alice Barkan
    • 1
  1. 1.Institute of Molecular BiologyUniversity of OregonEugeneUSA

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