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Genome-Wide Analysis of RNA-Protein Interactions in Plants

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Plant Systems Biology

Part of the book series: Methods in Molecular Biology™ ((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.

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Notes

  1. 1.

    Considerable progress was made in this field between the time of manuscript submission and the time of publication. Therefore, several important recent studies are not discussed.

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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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  1. Institute of Molecular Biology, University of Oregon, Eugene, OR, USA

    Alice Barkan

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    Barkan, A. (2009). Genome-Wide Analysis of RNA-Protein Interactions in Plants. In: Belostotsky, D. (eds) Plant Systems Biology. Methods in Molecular Biology™, vol 553. Humana Press. https://doi.org/10.1007/978-1-60327-563-7_2

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