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Related Concept Videos

RNA-seq03:21

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Related Experiment Video

Updated: Mar 24, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Genome-Wide Profiling of RNA-Protein Interactions Using CLIP-Seq.

Cheryl Stork1, Sika Zheng2

  • 1Division of Biomedical Sciences, School of Medicine, University of California at Riverside, 201 SOMRB, 900 University Avenue, Riverside, CA, 92521, USA.

Methods in Molecular Biology (Clifton, N.J.)
|March 12, 2016
PubMed
Summary
This summary is machine-generated.

Individual nucleotide resolution CLIP (iCLIP) precisely maps protein-RNA interactions. This method refines UV crosslinking immunoprecipitation (CLIP) for accurate crosslinking site identification in RNA-binding proteins.

Keywords:
ImmunoprecipitationRBP–RNA complexRNA binding proteinsUV crosslinking immunoprecipitationiCLIP

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Protein-RNA interactions are crucial for cellular processes.
  • UV crosslinking immunoprecipitation (CLIP) is a key method for studying these interactions.
  • Standard CLIP methods face challenges in precise crosslinking site identification due to cDNA truncations and mutations.

Purpose of the Study:

  • To detail the procedure for individual nucleotide resolution CLIP (iCLIP).
  • To overcome limitations of standard CLIP for accurate mapping of protein-bound RNA.
  • To enable nucleotide-level resolution of RNA-binding protein crosslinking sites.

Main Methods:

  • UV crosslinking of proteins to RNA in cells or tissues.
  • Immunoprecipitation of protein-RNA complexes using specific antibodies.
  • Partial RNase digestion and protease digestion.
  • cDNA synthesis with circularization to capture truncated products.
  • High-throughput sequencing of cDNA libraries.

Main Results:

  • iCLIP enables precise identification of crosslinking sites at single nucleotide resolution.
  • The method overcomes challenges associated with cDNA truncations and mutations at crosslink sites.
  • Circularization of cDNA enhances sequencing adapter ligation efficiency.

Conclusions:

  • iCLIP provides a robust protocol for high-resolution mapping of RNA-binding protein targets.
  • This technique significantly improves the accuracy of identifying functional protein-RNA binding sites.
  • iCLIP is essential for detailed studies of gene regulation and RNA processing.