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RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts

Nature Protocols volume 1, pages 302–307 (2006)Cite this article

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Abstract

RNA targets of multitargeted RNA-binding proteins (RBPs) can be studied by various methods including mobility shift assays, iterative in vitro selection techniques and computational approaches. These techniques, however, cannot be used to identify the cellular context within which mRNAs associate, nor can they be used to elucidate the dynamic composition of RNAs in ribonucleoprotein (RNP) complexes in response to physiological stimuli. But by combining biochemical and genomics procedures to isolate and identify RNAs associated with RNA-binding proteins, information regarding RNA–protein and RNA–RNA interactions can be examined more directly within a cellular context. Several protocols — including the yeast three-hybrid system and immunoprecipitations that use physical or chemical cross-linking — have been developed to address this issue. Cross-linking procedures in general, however, are limited by inefficiency and sequence biases. The approach outlined here, termed RNP immunoprecipitation–microarray (RIP-Chip), allows the identification of discrete subsets of RNAs associated with multi-targeted RNA-binding proteins and provides information regarding changes in the intracellular composition of mRNPs in response to physical, chemical or developmental inducements of living systems. Thus, RIP-Chip can be used to identify subsets of RNAs that have related functions and are potentially co-regulated, as well as proteins that are associated with them in RNP complexes. Using RIP-Chip, the identification and/or quantification of RNAs in RNP complexes can be accomplished within a few hours or days depending on the RNA detection method used.

*Note: In the version of the article originally published, in the last sentence of the ANTICIPATED RESULTS section, the callout should be to reference 19 instead of 18. The error has been corrected in the HTML and PDF versions of the article.

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Change history

  • 31 August 2006

    In the version of the article originally published, in the last sentence of the ANTICIPATED RESULTS section, the callout should be to reference 19 instead of 18. The error has been corrected in the HTML and PDF versions of the article.

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Authors and Affiliations

  1. Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Jack D Keene, Jordan M Komisarow & Matthew B Friedersdorf

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  1. Jack D Keene
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  2. Jordan M Komisarow
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Correspondence to Jack D Keene, Jordan M Komisarow or Matthew B Friedersdorf.

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Competing interests

J.D.K. holds stock in Ribonomics, Inc., a company that owns patents for the RIP-Chip technology.

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Keene, J., Komisarow, J. & Friedersdorf, M. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1, 302–307 (2006). https://doi.org/10.1038/nprot.2006.47

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