HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Protein - RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome- wide means of mapping protein - RNA binding sites in vivo, by high- throughput sequencing of RNA isolated by crosslinking immunoprecipitation ( HITS- CLIP). HITS- CLIP analysis of the neuron- specific splicing factor Nova revealed extremely reproducible RNA- binding maps in multiple mouse brains. These maps provide genome- wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS- CLIP revealed a large number of Nova - RNA interactions in 39 untranslated regions, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS- CLIP, therefore, provides a robust, unbiased means to identify functional protein - RNA interactions in vivo.