To understand the function of RNA-binding proteins it is important to identify where proteins bind across the transcriptome. To do this we use a specialised RNA-Seq method, CLIP-Seq. The exact binding sites of a protein are identified by immunoprecipiating the protein of interest and its associated RNA molecules. The footprints of the protein are revealed by RNase digestion of unprotected fragments and these footprints are then sequenced.
The structure of RNA molecules is key to understanding RNA activity and function. This is true for both coding mRNAs and non-coding RNAs. SHAPE-Seq profiles the structure of RNA globally. This method involves the modification of RNA molecules by selective 2′-hydroxyl acylation, preferentially at flexible regions, which is then analyzed by primer extension (SHAPE). The primer extension products can be sequenced for a transcriptome-wide assessment, termed SHAPE-Seq.