The study of gene regulation in cells has recently begun to shift from a period dominated by the study of transcription factor‐DNA interactions to a new focus on RNA regulation. This was sparked by the still‐emerging recognition of the central role for RNA in cellular complexity emanating from the RNA World hypothesis, and has been facilitated by technologic advances, in particular high throughput RNA sequencing and crosslinking methods (RNA‐Seq, CLIP, and HITS‐CLIP). This study will place these advances in context, and, focusing on CLIP, will explain the method, what it can be used for, and how to approach using it. Examples of the successes, limitations, and future of the technique will be discussed. Copyright © 2010 John Wiley & Sons, Ltd.

This article is categorized under:

• RNA Methods > RNA Analyses In Vitro and In Silico
• RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
• Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
• RNA Methods > RNA Analyses in Cells