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NOVA2 and NOVA1 HITS-CLIP in wild-type mouse cortex (E18.5)

ABSTRACT: Mouse cortex samples from E18.5 wild-type were subjected to HITS-CLIP to detect NOVA2 and NOVA1 binding positions on RNA

ORGANISM(S): Mus musculus

PROVIDER: GSE69710 | GEO | 2016/05/26

SECONDARY ACCESSION(S): PRJNA286234

REPOSITORIES: GEO

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Project description:NOVA2 and NOVA1 HITS-CLIP in wild-type mouse cortex (E18.5)

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Wild type vs. Nova2 KO mouse: Exon array data

Project description:To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. 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 Nova2 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 3’ UTRs, 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.

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