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Updated: Jun 20, 2025

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Published on: July 2, 2010

Characterization of RVFV Nucleocapsid Protein Binding Sites on RNA by iCLIP-seq.

Miyuki Hayashi^1,2, J Stephen Lodmell^3,4

¹Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|July 22, 2024

Summary

Rift Valley fever virus nucleocapsid protein (N) interactions with RNA were studied. Individual nucleotide resolution, cross-linking, immunoprecipitation, and sequencing (iCLIP-seq) identified host and viral RNA motifs bound by N.

Keywords:

Nucleocapsid protein RNA Rift Valley fever virus iCLIP

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Last Updated: Jun 20, 2025

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Published on: July 2, 2010

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

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Published on: April 30, 2011

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Area of Science:

Virology
Molecular Biology
Genomics

Background:

The Rift Valley fever virus nucleocapsid protein (N) is crucial for viral RNA processes.
Understanding N protein-RNA interactions is key to deciphering viral mechanisms.

Purpose of the Study:

To detail a method for studying protein-RNA interactions during viral infection.
To identify host and viral RNA elements interacting with the N protein.

Main Methods:

The chapter explains the individual nucleotide resolution, cross-linking, immunoprecipitation, and sequencing (iCLIP-seq) technique.
This method allows for high-resolution mapping of protein-RNA binding sites.

Main Results:

iCLIP-seq can identify specific interactions between the N protein and both host and viral RNAs.
The method is capable of pinpointing RNA motifs that bind to the N protein.

Conclusions:

iCLIP-seq is a powerful tool for dissecting viral protein-RNA interactions in their native context.
This approach aids in understanding the role of RNA binding in viral function and pathogenesis.