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Nat Struct Mol Biol. 2012 Nov;19(11):1124-31. doi: 10.1038/nsmb.2420. Epub 2012 Oct 21.

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.

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1
Institut de Biologie de l'Ecole Normale Supérieure, Section de Génomique Fonctionnelle, Paris, France.

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.

PMID:
23085716
DOI:
10.1038/nsmb.2420
[Indexed for MEDLINE]

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