GO:0035145 exon-exon junction complex: Components, Assembly and Research Methods, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0035145 (exon-exon junction complex, EJC) is a multi-subunit complex deposited by the spliceosome ~20-24 nucleotides upstream of mRNA exon-exon junctions.
• The EJC is a central binding platform that coordinates mRNA export, translation, and nonsense-mediated mRNA decay (NMD).
• Core EJC components include EIF4A3, RBM8A (Y14), MAGOH, and CASC3 (MLN51), with additional factors such as UPF3B and SRRT.
• EJCs shape the m6A epitranscriptome and influence translation efficiency and mRNA stability.
• Dysregulation of EJC genes is linked to cancer, neurodevelopmental disorders, and neurological disease.
• CRISPR knockout, point mutation, knock-in, and overexpression models enable causal dissection of EJC gene function.
Description
The exon-exon junction complex (EJC) is a multi-subunit protein complex that is deposited by the spliceosome onto messenger RNA (mRNA) approximately 20-24 nucleotides upstream of exon-exon junctions. This deposition occurs during pre-mRNA splicing and marks spliced mRNAs for downstream regulation. The EJC serves as a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay (NMD), thereby influencing mRNA fate from the nucleus to the cytoplasm. Because of its central role in post-transcriptional gene regulation, the EJC is a key area of study for researchers investigating RNA processing, translation, and mRNA quality control. Understanding the EJC is also important for disease research, as mutations in EJC components have been associated with developmental disorders and cancer.
exon-exon junction complex At A Glance
| GO ID | GO:0035145 |
|---|---|
| GO term | exon-exon junction complex |
| Ontology | cellular_component |
| Synonym | EJC, exon junction complex |
| Major function | Binding platform for mRNA export and nonsense-mediated mRNA decay factors |
| Deposition site | Upstream of exon-exon junctions on spliced mRNA |
| Core components | EIF4A3, RBM8A, MAGOH, CASC3 |
| Associated processes | mRNA export, translation, NMD, m6A epitranscriptome regulation |
What Is GO:0035145?
According to the Gene Ontology, GO:0035145 (exon-exon junction complex) is defined as a multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. In simpler terms, it is a protein assembly that sits on newly spliced mRNAs and helps decide their fate, including where they go and whether they are degraded.
Why Is exon-exon junction complex Important in Cell Biology?
The exon-exon junction complex is essential for post-transcriptional gene regulation because it marks spliced mRNAs and recruits factors that control mRNA export, translation, and degradation. Its role in nonsense-mediated mRNA decay helps eliminate aberrant transcripts, protecting cells from potentially harmful proteins. EJCs also influence the m6A epitranscriptome and translation efficiency, linking splicing to broader gene expression programs. Dysregulation of EJC components has been implicated in cancer, neurodevelopmental disorders, and neurological diseases, making the complex a significant research focus.
• Coordinates mRNA export from the nucleus to the cytoplasm.
• Recruits NMD factors to trigger degradation of aberrant mRNAs.
• Shapes the m6A RNA modification landscape and epitranscriptome.
• Modulates translation efficiency and mRNA stability.
• Essential for normal development and tissue homeostasis.
• Mutations in EJC genes are linked to neurodevelopmental disorders.
• Altered EJC function is observed in various cancers.
• Provides a model for studying coupling of splicing with downstream RNA processes.
• Enables research on mRNA quality control mechanisms.
• Serves as a target for therapeutic intervention in diseases of RNA dysregulation.
What Happens During exon-exon junction complex?
Spliceosome-mediated deposition
In simple terms: When an mRNA is spliced, a group of proteins is left behind at the junction like a stamp.
The EJC is deposited by the spliceosome onto mRNA approximately 20-24 nucleotides upstream of exon-exon junctions during pre-mRNA splicing. This deposition is a hallmark of spliced mRNAs and occurs co-transcriptionally.
mRNA export
In simple terms: The EJC helps the mRNA leave the nucleus and go to the cytoplasm.
The EJC provides a binding platform for factors involved in mRNA export, facilitating the transport of spliced mRNAs from the nucleus to the cytoplasm.
Nonsense-mediated mRNA decay (NMD)
In simple terms: If an mRNA has a premature stop signal, the EJC helps mark it for destruction.
EJCs recruit NMD factors such as UPF3B to trigger degradation of mRNAs containing premature termination codons, thereby preventing the production of truncated proteins.
Translation and m6A regulation
In simple terms: The EJC can influence how efficiently an mRNA is translated and how it is chemically modified.
The EJC shapes the m6A epitranscriptome and modulates translation efficiency, linking splicing to downstream gene expression control.
Key Genes Involved in GO:0035145 exon-exon junction complex
The following genes encode core and auxiliary components of the exon-exon junction complex, as well as factors that interact with it.
| Gene | Major Role | Research Relevance |
|---|---|---|
| EIF4A3 | Core EJC component; RNA helicase | Essential for EJC assembly and NMD |
| RBM8A | Core EJC component (Y14) | Mutations linked to thrombocytopenia-absent radius syndrome |
| MAGOH | Core EJC component | Required for EJC stability and function |
| CASC3 | Core EJC component (MLN51) | Enhances EJC assembly and NMD |
| UPF3B | NMD factor recruited by EJC | Mutations associated with intellectual disability |
| UPF2 | NMD factor interacting with EJC | Central to NMD activation |
| UPF1 | NMD factor | Key effector of mRNA degradation |
| SRRT | EJC-associated factor | Involved in mRNA processing |
| PYM1 | EJC-interacting protein | Facilitates EJC disassembly during translation |
| BTZ | EJC component in Drosophila | Model for EJC function in development |
| RNPS1 | EJC-associated splicing factor | Links splicing to NMD |
| SAP18 | EJC-associated factor | Part of the EJC interactome |
| DDX39B | Export factor interacting with EJC | Couples EJC to mRNA export |
| NXF1 | mRNA export receptor | Interacts with EJC for nuclear export |
| THOC | TREX complex component | Coordinates with EJC in mRNA export |
| SMG1 | NMD kinase | Phosphorylates UPF1 in EJC-dependent NMD |
| SMG5 | NMD factor | Promotes mRNA degradation |
How Is exon-exon junction complex Regulated?
The EJC is regulated at multiple levels, including its assembly during splicing, its disassembly during translation, and its post-translational modifications. EJC disassembly can occur independently of translation and is associated with stalled ribosomes. The complex also exhibits modularity, with different subunits contributing to distinct functions.
exon-exon junction complex and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| RBM8A | Thrombocytopenia-absent radius syndrome | Knockout mouse, patient-derived iPSCs |
| UPF3B | Intellectual disability | Knockout mouse, neuronal cultures |
| EIF4A3 | Cancer progression | Cancer cell lines, xenograft models |
| MAGOH | Developmental defects | Zebrafish knockout, mouse models |
| CASC3 | Cancer and RNA dysregulation | CRISPR knockout cell lines |
Cancer
Dysregulation of EJC components such as EIF4A3 and RBM8A has been observed in various cancers, where they can influence proliferation, apoptosis, and metastasis through altered mRNA processing and NMD.
Neurodevelopmental disorders
Mutations in EJC-associated genes, including RBM8A and UPF3B, are linked to neurodevelopmental disorders such as thrombocytopenia-absent radius syndrome and intellectual disability.
Neurological disease
EJC components play roles in the central nervous system, and their dysfunction has been implicated in neurological conditions, including neurodegeneration.
From exon-exon junction complex-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of EIF4A3 affect NMD? | EIF4A3 knockout cell line |
| How do point mutations in RBM8A affect EJC assembly? | RBM8A point-mutation knock-in |
| What is the effect of EJC component overexpression? | Overexpression cell model |
| Where does the EJC localize in cells? | Tagged knock-in with fluorescent tag |
| Which mRNAs are regulated by the EJC? | RNA-seq after EJC knockdown |
| How does EJC dysfunction affect neuronal development? | Neuronal differentiation from knockout iPSCs |
How to Study the exon-exon junction complex Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Gene expression changes | EJC knockdown/knockout effects |
| Ribo-seq | Translation efficiency | EJC role in translation |
| RIP-seq | mRNA binding sites | Identifying EJC targets |
| Proteomics | Protein interactions | EJC complex composition |
| CRISPR screening | Gene essentiality | Identifying EJC-related pathways |
| Fluorescence microscopy | Protein localization | EJC dynamics |
| m6A-seq | m6A modification landscape | EJC shaping epitranscriptome |
RNA immunoprecipitation (RIP)
RIP can identify mRNAs bound by EJC components, revealing the repertoire of EJC targets.
Ribo-seq
Ribo-seq measures translation efficiency and can reveal how EJC components influence protein synthesis.
Proteomics
Mass spectrometry-based proteomics can identify EJC interaction partners and post-translational modifications.
Imaging
Fluorescence microscopy of tagged EJC components allows visualization of EJC localization and dynamics in living cells.
How CRISPR Can Be Used to Study GO:0035145 exon-exon junction complex
Knockout
CRISPR knockout of EJC genes such as EIF4A3 or RBM8A can reveal their essential roles in mRNA export, NMD, and cell viability.
Point Mutation
Point mutations in EJC genes can model disease-associated variants and dissect domain-specific functions.
Knock-in
Knock-in of tagged EJC components enables live-cell imaging and biochemical purification of the complex.
Overexpression
Overexpression of EJC components can test gain-of-function effects and interactions with the m6A machinery.
How EDITGENE Supports exon-exon junction complex Research
Researchers studying exon-exon junction complex-related genes often need to determine whether a candidate gene is causally involved in mRNA regulation, disease, or development. EDITGENE provides a comprehensive suite of CRISPR-based services to enable such investigations.
Contact EDITGENE today to design your custom CRISPR model for exon-exon junction complex research.
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PYM1 Knockout HEK293 Cell Line | EDJ-KQ3410 | Human | 84305 | Details Get a Quote |
| BCLAF1 Knockout HEK293 Cell Line | EDJ-KQ6742 | Human | 9774 | Details Get a Quote |
| THRAP3 Knockout HEK293 Cell Line | EDJ-KQ6843 | Human | 9967 | Details Get a Quote |
| CASC3 Knockout HEK293 Cell Line | EDJ-KQ7678 | Human | 22794 | Details Get a Quote |
| ACIN1 Knockout HEK293 Cell Line | EDJ-KQ7764 | Human | 22985 | Details Get a Quote |
| CCDC9 Knockout HEK293 Cell Line | EDJ-KQ8397 | Human | 26093 | Details Get a Quote |
| R3HCC1L Knockout HEK293 Cell Line | EDJ-KQ8747 | Human | 27291 | Details Get a Quote |
| TDRD3 Knockout HEK293 Cell Line | EDJ-KQ9710 | Human | 81550 | Details Get a Quote |
| MAGOHB Knockout HEK293 Cell Line | EDJ-KQ14183 | Human | 55110 | Details Get a Quote |
| UPF3A Knockout HEK293 Cell Line | EDJ-KQ15242 | Human | 65110 | Details Get a Quote |
| UPF3B Knockout HEK293 Cell Line | EDJ-KQ16036 | Human | 65109 | Details Get a Quote |
| PYM1 Knockout A-549 Cell Line | EDJ-KQ25123 | Human | 84305 | Details Get a Quote |
| PYM1 Knockout HCT 116 Cell Line | EDJ-KQ25124 | Human | 84305 | Details Get a Quote |
| PYM1 Knockout HeLa Cell Line | EDJ-KQ25125 | Human | 84305 | Details Get a Quote |
| THRAP3 Knockout HCT 116 Cell Line | EDJ-KQ30032 | Human | 9967 | Details Get a Quote |
- 1
- 2
- Next Page »
Frequently Asked Questions About exon-exon junction complex
What is the exon-exon junction complex?
The exon-exon junction complex (EJC) is a multi-subunit protein complex deposited by the spliceosome upstream of mRNA exon-exon junctions, serving as a platform for mRNA export and nonsense-mediated decay.
What genes are involved in the exon-exon junction complex?
Core genes include EIF4A3, RBM8A, MAGOH, and CASC3, with additional factors such as UPF3B and SRRT.
What is the function of GO:0035145?
GO:0035145 describes the exon-exon junction complex, which provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
How is the exon-exon junction complex assembled?
The EJC is deposited by the spliceosome during pre-mRNA splicing, approximately 20-24 nucleotides upstream of exon-exon junctions.
What diseases are associated with exon-exon junction complex mutations?
Mutations in EJC genes are linked to cancer, neurodevelopmental disorders, and neurological diseases.
How can CRISPR be used to study the exon-exon junction complex?
CRISPR knockout, point mutation, knock-in, and overexpression models allow functional dissection of EJC genes.
What is the role of EIF4A3 in the exon-exon junction complex?
EIF4A3 is a core EJC component and RNA helicase essential for EJC assembly and NMD.
How does the exon-exon junction complex regulate mRNA export?
The EJC recruits export factors that facilitate transport of spliced mRNAs from the nucleus to the cytoplasm.
What is the relationship between the exon-exon junction complex and m6A?
The EJC shapes the m6A epitranscriptome, influencing mRNA modification and stability.
What methods are used to study the exon-exon junction complex?
Common methods include RNA-seq, Ribo-seq, RIP-seq, proteomics, and fluorescence microscopy.
Conclusion
The exon-exon junction complex (GO:0035145) is a critical regulator of mRNA fate, coordinating export, translation, and nonsense-mediated decay. Its roles in development and disease make it a compelling target for research. CRISPR-based models and advanced omics approaches continue to unravel its mechanisms, offering insights into RNA biology and potential therapeutic avenues.
References
- 1. Yang X et al.. 2022. Exon junction complex shapes the m(6)A epitranscriptome.. Nat Commun 13(1):7904 PMID: 36550132
- 2. Abshire ET et al.. 2025. Gene regulation through exon junction complex modularity.. Nat Struct Mol Biol 32(12):2387-2397 PMID: 41339861
- 3. Asthana S et al.. 2022. The Physiological Roles of the Exon Junction Complex in Development and Diseases.. Cells 11(7) PMID: 35406756
- 4. Schlautmann LP et al.. 2020. A Day in the Life of the Exon Junction Complex.. Biomolecules 10(6) PMID: 32517083
- 5. Woodward LA et al.. 2017. The exon junction complex: a lifelong guardian of mRNA fate.. Wiley Interdiscip Rev RNA 8(3) PMID: 28008720
- 6. Bensaude O et al.. 2024. Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly.. Nat Commun 15(1):4209 PMID: 38760352
- 7. Gerbracht JV et al.. 2018. The exon junction complex: structural insights into a faithful companion of mammalian mRNPs.. Biochem Soc Trans 46(1):153-161 PMID: 29351963
- 8. Bartkowska K et al.. 2018. Roles of the exon junction complex components in the central nervous system: a mini review.. Rev Neurosci 29(8):817-824 PMID: 29791316
