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| Status |
Public on Oct 21, 2012 |
| Title |
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Saulière J, Murigneux V, Wang Z, Marquenet E, Barbosa I, Le Tonquèze O, Audic Y, Paillard L, Roest Crollius H, Le Hir H |
| Citation(s) |
23085716 |
| Submission date |
Sep 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Herve LE HIR |
| E-mail(s) |
lehir@ens.fr
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| Organization name |
IBENS
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| Department |
Functional Genomics
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| Lab |
Le Hir lab
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| Street address |
46 rue d'Ulm
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| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA174879 |
| SRA |
SRP015711 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40778_RAW.tar |
140.0 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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