Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.
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
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.
other, RNA-seq of coding RNA
Herve LE HIR <firstname.lastname@example.org>, 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. Sauliï¿½re J, Murigneux V, Wang Z, Marquenet E, Barbosa I, Le Tonquï¿½ze O, Audic Y, Paillard L, Roest Crollius H, Le Hir H. , PMID:23085716