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

Jérôme Saulière (1) , Valentine Murigneux (2) , Zhen Wang (3) , Emélie Marquenet (2) , Isabelle Barbosa (4) , Olivier Le Tonquèze (5, 6) , Yann Audic (5, 6) , Luc Paillard (5, 6) , Hugues Roest Crollius (2) , Hervé Le Hir (2)

1 CGM - Centre de génétique moléculaire
2 IBENS - Institut de biologie de l'ENS Paris
3 Nankai University
4 CRRET - Croissance cellulaire, réparation et régénération tissulaires
5 UEB - Université européenne de Bretagne - European University of Brittany
6 IGDR - Institut de Génétique et Développement de Rennes

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.

Domaines: Biologie moléculaire

Jérôme Saulière, Valentine Murigneux, Zhen Wang, Emélie Marquenet, Isabelle Barbosa, et al.. CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.. Nature Structural and Molecular Biology, 2012, 19 (11), pp.1124-31. ⟨10.1038/nsmb.2420⟩. ⟨hal-00982626⟩