title: Transcriptome-wide identification of RNA binding sites by CLIP-seq.
abstract: An emergent strategy for the transcriptome-wide study of protein-RNA interactions is CLIP-seq (crosslinking and immunoprecipitation followed by high-throughput sequencing). We combined CLIP-seq and mRNA-seq to identify direct RNA binding sites of eIF4AIII in human cells. This RNA helicase is a core constituant of the Exon Junction Complex (EJC), a multifunctional protein complex associated with spliced mRNAs in metazoans. Here, we describe the successive steps of the CLIP protocol and the computational tools and strategies we employed to map the physiological targets of eIF4AIII on human RNAs.
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, Section de Génomique Fonctionnelle, Paris, France; CNRS UMR8197, Paris, France; INSERM U1024, Paris, France.
authors.forename: Valentine
authors.initials: V
authors.lastname: Murigneux
authors.forename: Jérôme
authors.initials: J
authors.lastname: Saulière
authors.forename: Hugues
authors.initials: H
authors.lastname: Roest Crollius
authors.forename: Hervé
authors.initials: H
authors.lastname: Le Hir
mesh_terms: D001665:Binding Sites; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012326:RNA Splicing / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D016601:RNA-Binding Proteins
keywords: Bioinformatics; CLIP; Next-generation sequencing; Protein–RNA interactions