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RNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs

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RNA Detection and Visualization

Part of the book series: Methods in Molecular Biology ((MIMB,volume 714))

Abstract

Post-transcriptional gene regulation is largely mediated by RNA-binding proteins (RBPs) that modulate mRNA expression at multiple levels, from RNA processing to translation, localization, and degradation. Thereby, the genome-wide identification of mRNAs regulated by RBPs is crucial to uncover post-­transcriptional gene regulatory networks. In this chapter, we provide a detailed protocol for one of the techniques that has been developed to systematically examine RNA targets for RBPs. This technique involves the purification of endogenously formed RBP–mRNA complexes with specific antibodies from cellular extracts, followed by the identification of associated RNAs using DNA microarrays. Such RNA-binding protein immunopurification-microarray profiling, also called RIP-Chip, has also been applied to identify mRNAs that are transported to distinct subcellular compartments by RNP–motor complexes. The application and further development of this method could provide global insights into the subcellular architecture of the RBP–RNA network, and how it is restructured upon changing environmental conditions, during development, and possibly in disease.

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Authors and Affiliations

  1. Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland

    André P. Gerber

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  1. Alessia Galgano
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  2. André P. Gerber
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Correspondence to André P. Gerber .

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Editors and Affiliations

  1. , Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel

    Jeffrey E. Gerst

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Galgano, A., Gerber, A.P. (2011). RNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs. In: Gerst, J. (eds) RNA Detection and Visualization. Methods in Molecular Biology, vol 714. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-005-8_23

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  • DOI: https://doi.org/10.1007/978-1-61779-005-8_23

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-004-1

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