CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.
Nat Struct Mol Biol, 2012/11;19(11):1124-31.
Saulière J[1], Murigneux V, Wang Z, Marquenet E, Barbosa I, Le Tonquèze O, Audic Y, Paillard L, Roest Crollius H, Le Hir H
Affiliations
PMID: 23085716DOI: 10.1038/nsmb.2420
Impact factor: 18.361
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.
MeSH terms
Binding Sites; Chromosome Mapping; Eukaryotic Initiation Factor-4A; Exons; High-Throughput Nucleotide Sequencing; Humans; Immunoprecipitation; Multiprotein Complexes; RNA, Messenger; Transcriptome
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