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Post-Transcriptional Gene Regulation pp 167–188Cite as

PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites

Part of the Methods in Molecular Biology book series (MIMB,volume 2404)

Abstract

During post-transcriptional gene regulation (PTGR), RNA binding proteins (RBPs) interact with all classes of RNA to control RNA maturation, stability, transport, and translation. Here, we describe Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a transcriptome-scale method for identifying RBP binding sites on target RNAs with nucleotide-level resolution. This method is readily applicable to any protein directly contacting RNA, including RBPs that are predicted to bind in a sequence- or structure-dependent manner at discrete RNA recognition elements (RREs), and those that are thought to bind transiently, such as RNA polymerases or helicases.

Key words

  • RNA binding protein (RBP)
  • RNA
  • Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP)
  • Crosslinking and Immunoprecipitation (CLIP)
  • Post-transcriptional gene regulation (PTGR)
  • RNA recognition element (RRE)
  • Non-coding RNA
  • mRNA
  • Binding site

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Author notes

  1. Charles Danan and Sudhir Manickavel contributed equally to this work.

Authors and Affiliations

  1. RNA Molecular Biology Group, NIAMS, Bethesda, MD, USA

    Charles Danan, Sudhir Manickavel & Markus Hafner

Authors
  1. Charles Danan
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  2. Sudhir Manickavel
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  3. Markus Hafner
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Corresponding author

Correspondence to Markus Hafner .

Editor information

Editors and Affiliations

  1. Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

    Dr. Erik Dassi

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Danan, C., Manickavel, S., Hafner, M. (2022). PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. In: Dassi, E. (eds) Post-Transcriptional Gene Regulation. Methods in Molecular Biology, vol 2404. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1851-6_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1851-6_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1850-9

  • Online ISBN: 978-1-0716-1851-6

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