CLIP-Seq

Principle

CLIP-Seq captures interaction regions between RNA and RNA-binding proteins using crosslinking immunoprecipitation and sequencing. It supports investigation of binding distributions, sequence preferences, splicing, RNA stability and related post-transcriptional processes.

Applications

• Identify candidate RBP-binding regions on RNA
• Investigate binding motifs and sequence preferences
• Relate splicing-factor binding to post-transcriptional regulation

Method features

• Crosslinking supports studies of cellular RNA-protein interactions
• Focuses more directly on binding regions than conventional enrichment
• Crosslinking, antibody and library strategies depend on the target RBP

Workflow

1. 01

   Select the RBP, antibody and crosslinking strategy

2. 02

   Crosslink and immunoenrich RNA-protein complexes

3. 03

   Recover RNA fragments, prepare libraries and sequence

4. 04

   Identify binding regions and annotate motifs and transcripts

This is a workflow overview. Experimental and analytical details depend on sample conditions and research objectives.