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RNA-binding protein immunopurification-microarray (RIP-Chip) analysis to profile localized RNAs.

Galgano, A and Gerber, AP (2011) RNA-binding protein immunopurification-microarray (RIP-Chip) analysis to profile localized RNAs. Methods Mol Biol, 714. pp. 369-385.

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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.

Item Type: Article
Divisions : Surrey research (other units)
Authors : Galgano, A and Gerber, AP
Date : 2011
DOI : 10.1007/978-1-61779-005-8_23
Uncontrolled Keywords : Animals, Antibodies, Antibody Specificity, Cell Extracts, Color, Edetic Acid, Fluorescent Dyes, Humans, Microspheres, Nerve Tissue Proteins, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, RNA, RNA Transport, RNA, Antisense, RNA-Binding Proteins, Ribonucleoproteins, Sepharose, Staphylococcal Protein A, Time Factors
Depositing User : Symplectic Elements
Date Deposited : 28 Mar 2017 14:39
Last Modified : 24 Jan 2020 11:36

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