Transcriptomics

Dataset Information

362

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


ABSTRACT: 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.

ORGANISM(S): Homo sapiens  

SUBMITTER: Luc Paillard   Olivier Le Tonquèze  Zhen Wang  Valentine Murigneux  Hugues Roest Crollius  Emélie Marquenet  Yann Audic  Isabelle Barbosa  Hervé Le Hir  Jérôme Saulière  Herve LE HIR 

PROVIDER: E-GEOD-40778 | ArrayExpress | 2012-10-21

SECONDARY ACCESSION(S): SRP015711GSE40778PRJNA174879

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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

Saulière Jérôme J   Murigneux Valentine V   Wang Zhen Z   Marquenet Emélie E   Barbosa Isabelle I   Le Tonquèze Olivier O   Audic Yann Y   Paillard Luc L   Roest Crollius Hugues H   Le Hir Hervé H  

Nature structural & molecular biology 20121021 11


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  ...[more]

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