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

Article

关键词: PRE-MESSENGER-RNA;    BINDING PROTEIN;    NOVA;    POLYADENYLATION;    GENE;    IDENTIFICATION;    NETWORK;    DISEASE;    ANTIGEN;    TARGET;   

DOI  :  10.1038/nature07488

来源: SCIE

【 摘 要 】

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.

【 授权许可】

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