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

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

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

Abstract:

The nucleocapsid protein (N) in Rift Valley fever virus is an RNA-binding protein that functions in viral transcription, replication, and packaging. In this chapter, the method for studying protein-RNA interactions in context of viral infection using individual nucleotide resolution, cross-linking, immunoprecipitation, and sequencing (iCLIP-seq) is explained. The method is useful for identifying the interactions between both host and viral RNAs with N and can identify RNA motifs that interact with the protein of interest.

Keywords:

Nucleocapsid protein RNA Rift Valley fever virus iCLIP

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