ArticleNature structural & molecular biology2012
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.
Article in Nature structural & molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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Who cites it
133 citing papers in PubMed, 210 citations in OpenAlex.
- A systems perspective on monoallelic inborn errors of immunity.Nature genetics · 2026Review
- Assembly of exon junction complexes on spliceosomes begins before spliceosome activation.Nucleic acids research · 2026Article
- Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants.Nature genetics · 2026Article
- Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay.bioRxiv : the preprint server for biology · 2025Article
- Gene regulation through exon junction complex modularity.Nature structural & molecular biology · 2025Review
- Chemical inhibition of exon junction complex assembly impairs mRNA localization and neural stem cells ciliogenesis.Nucleic acids research · 2025Article
- FLAG Immunoprecipitation-Based Mapping of the In Vivo Assembled Spliceosomal C* Complex.International journal of molecular sciences · 2025Article
- PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.Nature communications · 2025Article
- Regulatory roles of circular RNAs in Wnt and other oncogenic signaling pathways in breast cancer progression: a comprehensive review.European journal of medical research · 2025Review
- ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA.Nucleic acids research · 2025Article
- Exon junction complexes regulate osteoclast-induced bone resorption by influencing the NFATc1 m6A distribution through the "shield effect".Clinical and translational medicine · 2025Article
- Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns.Nucleic acids research · 2025Article
- Decoding protein-RNA interactions using CLIP-based methodologies.Nature reviews. Genetics · 2024Review
- Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.Molecular cell · 2024Article
- Defenders of the Transcriptome: Guard Protein-Mediated mRNA Quality Control inInternational journal of molecular sciences · 2024Review
- Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly.Nature communications · 2024Article
- mRNA accessibility within mRNPs as a determinant of gene expression.Trends in biochemical sciences · 2024Review
- Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila.BMC biology · 2023Article
- The long and short of EJC-independent nonsense-mediated RNA decay.Biochemical Society transactions · 2023Review
- Hsa_circ_0060467 promotes breast cancer liver metastasis by complexing with eIF4A3 and sponging miR-1205.Cell death discovery · 2023Article
73 more citing papers are in PubMed but not listed here.
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10 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.