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E-GEOD-40778 - CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

Released on 21 October 2012, last updated on 11 March 2013
Homo sapiens
Samples (3)
Protocols (6)
The exon junction complex (EJC) is a central effector of mRNAs fate, linking nuclear processing to mRNA transport, translation and surveillance. Little is known about its transcriptome-wide targets. We used high-throughput sequencing after crosslinking and immunoprecipitation (HITS-CLIP) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks mainly located in spliced mRNAs. Most expressed exons harbour peaks equally distributed between the canonical EJC region ∼24 nucleotides upstream of exonic junctions and other non-canonical regions. Unexpectedly, both are preferentially associated to unstructured and purine-rich sequences containing the motif GAAGA, a potential binding site of 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. To identify direct RNA binding sites of the EJC core component eIF4AIII, two biological CLIP-seq replicates were performed in HeLa cells. Additionally, mRNA-seq of the HeLa transcriptome was performed to normalize for the mRNA expression levels.
Experiment types
other, RNA-seq of coding RNA 
Herve LE HIR <>, Emélie Marquenet, Hervé Le Hir, Hugues Roest Crollius, Isabelle Barbosa, Jérôme Saulière, Luc Paillard, Olivier Le Tonquèze, Valentine Murigneux, Yann Audic, Zhen Wang
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Sauli�re J, Murigneux V, Wang Z, Marquenet E, Barbosa I, Le Tonqu�ze O, Audic Y, Paillard L, Roest Crollius H, Le Hir H. , PMID:23085716
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-40778.idf.txt
Sample and data relationshipE-GEOD-40778.sdrf.txt
Processed data (2),