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PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins

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mRNA Decay

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1720))

Abstract

RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A variety of experimental approaches have been developed to characterize the RNAs associated with RBPs in vitro as well as in vivo. Our laboratory developed Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP), which in combination with next-generation sequencing enables the identification of RNA targets of RBPs at a nucleotide-level resolution. Here we present an updated and condensed step-by-step PAR-CLIP protocol followed by the description of our RNA-seq data analysis pipeline.

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Authors and Affiliations

  1. Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA

    Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer & Thomas Tuschl

Authors
  1. Aitor Garzia
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  2. Pavel Morozov
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  3. Marcin Sajek
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  4. Cindy Meyer
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  5. Thomas Tuschl
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Corresponding author

Correspondence to Thomas Tuschl .

Editor information

Editors and Affiliations

  1. Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia

    Shireen R. Lamandé

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Garzia, A., Morozov, P., Sajek, M., Meyer, C., Tuschl, T. (2018). PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins. In: Lamandé, S. (eds) mRNA Decay. Methods in Molecular Biology, vol 1720. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7540-2_5

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  • DOI: https://doi.org/10.1007/978-1-4939-7540-2_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7539-6

  • Online ISBN: 978-1-4939-7540-2

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