title: CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.
abstract: The exon junction complex (EJC) is a central effector of the fate of mRNAs, linking nuclear processing to mRNA transport, translation and surveillance. However, little is known about its transcriptome-wide targets. We used cross-linking and immunoprecipitation methods coupled to high-throughput sequencing (CLIP-seq) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks that are located mainly in spliced mRNAs. Most expressed exons harbor peaks either in the canonical EJC region, located ~24 nucleotides upstream of exonic junctions, or in other noncanonical regions. Notably, both of these types of peaks are preferentially associated with unstructured and purine-rich sequences containing the motif GAAGA, which is a potential binding site for EJC-associated factors. Therefore, EJC positions vary spatially and quantitatively between exons. This transcriptome-wide mapping of human eIF4AIII reveals unanticipated aspects of the EJC and broadens its potential impact on post-transcriptional regulation.
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, Section de Génomique Fonctionnelle, Paris, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Saulière
authors.forename: Valentine
authors.initials: V
authors.lastname: Murigneux
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.forename: Emélie
authors.initials: E
authors.lastname: Marquenet
authors.forename: Isabelle
authors.initials: I
authors.lastname: Barbosa
authors.forename: Olivier
authors.initials: O
authors.lastname: Le Tonquèze
authors.forename: Yann
authors.initials: Y
authors.lastname: Audic
authors.forename: Luc
authors.initials: L
authors.lastname: Paillard
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 / Q000235:genetics; D002874:Chromosome Mapping; D039601:Eukaryotic Initiation Factor-4A / Q000235:genetics* / Q000378:metabolism; D005091:Exons / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D046912:Multiprotein Complexes / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D046912:Multiprotein Complexes; D012333:RNA, Messenger; D039601:Eukaryotic Initiation Factor-4A