The EJC is deposited 24 nucleotides upstream of spliced junctions during splicing. It accompanies mRNAs from the nucleus to the cytoplasm, where it is removed by the first round of translation, and recycled back into the nucleus.
The core of the EJC consists of four proteins. Structural studies revealed that the DEAD-box RNA helicase eIF4A3 functions as a clamp that binds RNA in a sequence-unspecific manner. MAGOH and Y14 form a heterodimer to lock eIF4A3 onto the mRNA, whereas MLN51 contacts eIF4A3 and the mRNA and provides further stability.
The core complex acts as a binding platform for peripheral factors involved in splicing, transport, translation and nonsense-mediated decay (NMD). The composition of peripheral factors depends on the different stages of mRNA processing.
The EJC has several functions in regulating different post-transcriptional processes, including splicing, cellular localization, translation and NMD.
The EJC is not present at every exon junction, and it does not always bind at the canonical position. This differential loading could impact the composition and functions of different EJCs.
The EJC acts as a central node of post-transcriptional gene regulation, and changes in EJC protein expression levels lead to several developmental defects and diseases.
The exon junction complex (EJC) is deposited onto mRNAs following splicing and adopts a unique structure, which can both stably bind to mRNAs and function as an anchor for diverse processing factors. Recent findings revealed that in addition to its established roles in nonsense-mediated mRNA decay, the EJC is involved in mRNA splicing, transport and translation. While structural studies have shed light on EJC assembly, transcriptome-wide analyses revealed differential EJC loading at spliced junctions. Thus, the EJC functions as a node of post-transcriptional gene expression networks, the importance of which is being revealed by the discovery of increasing numbers of EJC-related disorders.
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Le Hir, H., Nott, A. & Moore, M. J. How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28, 215–220 (2003).
Maquat, L. E. When cells stop making sense: effects of nonsense codons on RNA metabolism in vertebrate cells. RNA 1, 453–465 (1995).
Hentze, M. W. & Kulozik, A. E. A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96, 307–310 (1999).
Shyu, A. B. & Wilkinson, M. F. The double lives of shuttling mRNA binding proteins. Cell 102, 135–138 (2000).
Kervestin, S. & Jacobson, A. NMD: a multifaceted response to premature translational termination. Nat. Rev. Mol. Cell Biol. 13, 700–712 (2012).
Schweingruber, C., Rufener, S. C., Zund, D., Yamashita, A. & Muhlemann, O. Nonsense-mediated mRNA decay — mechanisms of substrate mRNA recognition and degradation in mammalian cells. Biochim. Biophys. Acta 1829, 612–623 (2013).
Popp, M. W. & Maquat, L. E. Organizing principles of mammalian nonsense-mediated mRNA decay. Annu. Rev. Genet. 47, 139–165 (2013). References 5–7 provided the first evidence of splicing-dependent NMD in mammals.
Cheng, J., Belgrader, P., Zhou, X. & Maquat, L. E. Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance. Mol. Cell. Biol. 14, 6317–6325 (1994).
Carter, M. S., Li, S. & Wilkinson, M. F. A splicing-dependent regulatory mechanism that detects translation signals. EMBO J. 15, 5965–5975 (1996).
Thermann, R. et al. Binary specification of nonsense codons by splicing and cytoplasmic translation. EMBO J. 17, 3484–3494 (1998).
Zhang, J., Sun, X., Qian, Y., LaDuca, J. P. & Maquat, L. E. At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol. Cell. Biol. 18, 5272–5283 (1998).
Nagy, E. & Maquat, L. E. A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem. Sci. 23, 198–199 (1998).
Le Hir, H., Izaurralde, E., Maquat, L. E. & Moore, M. J. The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions. EMBO J. 19, 6860–6869 (2000). This study was the first to identify the EJCs, which are deposited following splicing 24 nt upstream of the spliced junctions.
Kataoka, N. et al. Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol. Cell 6, 673–682 (2000).
Le Hir, H., Gatfield, D., Izaurralde, E. & Moore, M. J. The exon–exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20, 4987–4997 (2001).
Luo, M. L. et al. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature 413, 644–647 (2001).
Kim, V. N. et al. The Y14 protein communicates to the cytoplasm the position of exon–exon junctions. EMBO J. 20, 2062–2068 (2001).
Lejeune, F., Ishigaki, Y., Li, X. & Maquat, L. E. The exon junction complex is detected on CBP80-bound but not eIF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling. EMBO J. 21, 3536–3545 (2002).
Dostie, J. & Dreyfuss, G. Translation is required to remove Y14 from mRNAs in the cytoplasm. Curr. Biol. 12, 1060–1067 (2002).
Gehring, N. H., Lamprinaki, S., Kulozik, A. E. & Hentze, M. W. Disassembly of exon junction complexes by PYM. Cell 137, 536–548 (2009).
Lykke-Andersen, J., Shu, M. D. & Steitz, J. A. Communication of the position of exon–exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 293, 1836–1839 (2001).
Kim, V. N., Kataoka, N. & Dreyfuss, G. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon–exon junction complex. Science 293, 1832–1836 (2001).
Wiegand, H. L., Lu, S. & Cullen, B. R. Exon junction complexes mediate the enhancing effect of splicing on mRNA expression. Proc. Natl Acad. Sci. USA 100, 11327–11332 (2003).
Nott, A., Le Hir, H. & Moore, M. J. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 18, 210–222 (2004).
Gehring, N. H., Neu-Yilik, G., Schell, T., Hentze, M. W. & Kulozik, A. E. Y14 and hUpf3b form an NMD-activating complex. Mol. Cell 11, 939–949 (2003).
Singh, G., Pratt, G., Yeo, G. W. & Moore, M. J. The clothes make the mRNA: past and present trends in mRNP fashion. Annu. Rev. Biochem. 84, 325–354 (2015).
Ballut, L. et al. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat. Struct. Mol. Biol. 12, 861–869 (2005).
Tange, T. O., Shibuya, T., Jurica, M. S. & Moore, M. J. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11, 1869–1883 (2005).
Fribourg, S., Gatfield, D., Izaurralde, E. & Conti, E. A novel mode of RBD-protein recognition in the Y14–Mago complex. Nat. Struct. Biol. 10, 433–439 (2003).
Singh, K. K., Wachsmuth, L., Kulozik, A. E. & Gehring, N. H. Two mammalian MAGOH genes contribute to exon junction complex composition and nonsense-mediated decay. RNA Biol. 10, 1291–1298 (2013).
Gong, P., Zhao, M. & He, C. Slow co-evolution of the MAGO and Y14 protein families is required for the maintenance of their obligate heterodimerization mode. PLoS ONE 9, e84842 (2014).
Degot, S. et al. Association of the breast cancer protein MLN51 with the exon junction complex via its speckle localizer and RNA binding module. J. Biol. Chem. 279, 33702–33715 (2004).
Daguenet, E. et al. Perispeckles are major assembly sites for the exon junction core complex. Mol. Biol. Cell 23, 1765–1782 (2012).
Andersen, C. B. et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313, 1968–1972 (2006).
Bono, F., Ebert, J., Lorentzen, E. & Conti, E. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126, 713–725 (2006). References 34 and 35 show crystal structures of the EJC complex, revealing that the binding of eIF4A3 to mRNAs is stabilized by the Magoh–Y14 heterodimer, and that MLN51 also contacts the mRNA and stabilizes the complex.
Linder, P. & Jankowsky, E. From unwinding to clamping — the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12, 505–516 (2011).
Nielsen, K. H. et al. Mechanism of ATP turnover inhibition in the EJC. RNA 15, 67–75 (2009).
Xiol, J. et al. RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts. Cell 157, 1698–1711 (2014).
Wahl, M. C., Will, C. L. & Luhrmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701–718 (2009).
Will, C. L. & Luhrmann, R. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 3, a003707 (2011).
Bessonov, S., Anokhina, M., Will, C. L., Urlaub, H. & Luhrmann, R. Isolation of an active step I spliceosome and composition of its RNP core. Nature 452, 846–850 (2008).
Reichert, V. L., Le Hir, H., Jurica, M. S. & Moore, M. J. 5′ exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly. Genes Dev. 16, 2778–2791 (2002).
Makarov, E. M. et al. Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science 298, 2205–2208 (2002).
Merz, C., Urlaub, H., Will, C. L. & Luhrmann, R. Protein composition of human mRNPs spliced in vitro and differential requirements for mRNP protein recruitment. RNA 13, 116–128 (2007).
Zhang, Z. & Krainer, A. R. Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components. Proc. Natl Acad. Sci. USA 104, 11574–11579 (2007).
Gehring, N. H., Lamprinaki, S., Hentze, M. W. & Kulozik, A. E. The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay. PLoS Biol. 7, e1000120 (2009).
Shibuya, T., Tange, T. O., Sonenberg, N. & Moore, M. J. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat. Struct. Mol. Biol. 11, 346–351 (2004).
Yeh, T. C. et al. Splicing factor Cwc22 is required for the function of Prp2 and for the spliceosome to escape from a futile pathway. Mol. Cell. Biol. 31, 43–53 (2011).
Alexandrov, A., Colognori, D., Shu, M. D. & Steitz, J. A. Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay. Proc. Natl Acad. Sci. USA 109, 21313–21318 (2012).
Barbosa, I. et al. Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes exon junction complex assembly. Nat. Struct. Mol. Biol. 19, 983–990 (2012).
Steckelberg, A. L., Boehm, V., Gromadzka, A. M. & Gehring, N. H. CWC22 connects pre-mRNA splicing and exon junction complex assembly. Cell Rep. 2, 454–461 (2012). References 49–51 show that CWC22 is a partner of eIF4A3 and facilitates its recruitment to the spliceosome; subsequent EJC assembly requires the dissociation of CWC22.
Buchwald, G., Schussler, S., Basquin, C., Le Hir, H. & Conti, E. Crystal structure of the human eIF4AIII–CWC22 complex shows how a DEAD-box protein is inhibited by a MIF4G domain. Proc. Natl Acad. Sci. USA 110, E4611–E4618 (2013).
Ideue, T., Sasaki, Y. T., Hagiwara, M. & Hirose, T. Introns play an essential role in splicing-dependent formation of the exon junction complex. Genes Dev. 21, 1993–1998 (2007).
De, I. et al. The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes. Nat. Struct. Mol. Biol. 22, 138–144 (2015).
Tange, T. O., Nott, A. & Moore, M. J. The ever-increasing complexities of the exon junction complex. Curr. Opin. Cell Biol. 16, 279–284 (2004).
Custodio, N. et al. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 10, 622–633 (2004).
Schmidt, U., Richter, K., Berger, A. B. & Lichter, P. In vivo BiFC analysis of Y14 and NXF1 mRNA export complexes: preferential localization within and around SC35 domains. J. Cell Biol. 172, 373–381 (2006).
Spector, D. L. & Lamond, A. I. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 3, a000646 (2011).
Blencowe, B. J., Issner, R., Nickerson, J. A. & Sharp, P. A. A coactivator of pre-mRNA splicing. Genes Dev. 12, 996–1009 (1998).
Sakashita, E., Tatsumi, S., Werner, D., Endo, H. & Mayeda, A. Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo. Mol. Cell. Biol. 24, 1174–1187 (2004).
Singh, K. K. et al. Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold. RNA 16, 2442–2454 (2010).
Schwerk, C. et al. ASAP, a novel protein complex involved in RNA processing and apoptosis. Mol. Cell. Biol. 23, 2981–2990 (2003).
Murachelli, A. G., Ebert, J., Basquin, C., Le Hir, H. & Conti, E. The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex. Nat. Struct. Mol. Biol. 19, 378–386 (2012).
Katahira, J. mRNA export and the TREX complex. Biochim. Biophys. Acta 1819, 507–513 (2012).
Kohler, A. & Hurt, E. Exporting RNA from the nucleus to the cytoplasm. Nat. Rev. Mol. Cell Biol. 8, 761–773 (2007).
Lykke-Andersen, J., Shu, M. D. & Steitz, J. A. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103, 1121–1131 (2000).
Serin, G., Gersappe, A., Black, J. D., Aronoff, R. & Maquat, L. E. Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4). Mol. Cell. Biol. 21, 209–223 (2001).
Kunz, J. B., Neu-Yilik, G., Hentze, M. W., Kulozik, A. E. & Gehring, N. H. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. RNA 12, 1015–1022 (2006).
Chamieh, H., Ballut, L., Bonneau, F. & Le Hir, H. NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Nat. Struct. Mol. Biol. 15, 85–93 (2008). This biochemical study shows that the EJC core binds to UPF3B, which serves as a bridge that binds to UPF2 and UPF1, thereby stimulating the RNA helicase activity of UPF1.
Buchwald, G. et al. Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC–UPF3b complex. Proc. Natl Acad. Sci. USA 107, 10050–10055 (2010).
Kashima, I. et al. Binding of a novel SMG-1–Upf1–eRF1–eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. Genes Dev. 20, 355–367 (2006). This study defines the stepwise assembly of NMD complexes in human.
Ohnishi, T. et al. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Mol. Cell 12, 1187–1200 (2003).
Kashima, I. et al. SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. Genes Dev. 24, 2440–2450 (2010).
Gehring, N. H. et al. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 20, 65–75 (2005). This study revealed that UPF2 is required for RNPS1-induced NMD but is dispensable for other EJC core-induced NMD activity.
Singh, N. N., Singh, R. N. & Androphy, E. J. Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes. Nucleic Acids Res. 35, 371–389 (2007).
Ma, X. M., Yoon, S. O., Richardson, C. J., Julich, K. & Blenis, J. SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. Cell 133, 303–313 (2008).
Fonseca, B. D. et al. The ever-evolving role of mTOR in translation. Semin. Cell Dev. Biol. 36, 102–112 (2014).
Singh, G. et al. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell 151, 750–764 (2012).
Sauliere, J. et al. CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Nat. Struct. Mol. Biol. 19, 1124–1131 (2012). Reference 78 and 79 report genome-wide studies that showed that EJC binding is not the same at different splice junctions, both within and between different mRNAs.
Long, J. C. & Caceres, J. F. The SR protein family of splicing factors: master regulators of gene expression. Biochem. J. 417, 15–27 (2009).
Buxbaum, A. R., Haimovich, G. & Singer, R. H. In the right place at the right time: visualizing and understanding mRNA localization. Nat. Rev. Mol. Cell Biol. 16, 95–109 (2015).
Bono, F. et al. Molecular insights into the interaction of PYM with the Mago–Y14 core of the exon junction complex. EMBO Rep. 5, 304–310 (2004).
Diem, M. D., Chan, C. C., Younis, I. & Dreyfuss, G. PYM binds the cytoplasmic exon–junction complex and ribosomes to enhance translation of spliced mRNAs. Nat. Struct. Mol. Biol. 14, 1173–1179 (2007).
Ghosh, S., Obrdlik, A., Marchand, V. & Ephrussi, A. The EJC binding and dissociating activity of PYM is regulated in Drosophila. PLoS Genet. 10, e1004455 (2014).
Chazal, P. E. et al. EJC core component MLN51 interacts with eIF3 and activates translation. Proc. Natl Acad. Sci. USA 110, 5903–5908 (2013).
Mingot, J. M., Kostka, S., Kraft, R., Hartmann, E. & Gorlich, D. Importin 13: a novel mediator of nuclear import and export. EMBO J. 20, 3685–3694 (2001).
Bono, F., Cook, A. G., Grunwald, M., Ebert, J. & Conti, E. Nuclear import mechanism of the EJC component Mago–Y14 revealed by structural studies of importin 13. Mol. Cell 37, 211–222 (2010).
Ashton-Beaucage, D. et al. The exon junction complex controls the splicing of MAPK and other long intron-containing transcripts in Drosophila. Cell 143, 251–262 (2010).
Roignant, J. Y. & Treisman, J. E. Exon junction complex subunits are required to splice Drosophila MAP kinase, a large heterochromatic gene. Cell 143, 238–250 (2010).
Ashton-Beaucage, D. & Therrien, M. The exon junction complex: a splicing factor for long intron containing transcripts? Fly 5, 224–233 (2011).
Hayashi, R., Handler, D., Ish-Horowicz, D. & Brennecke, J. The exon junction complex is required for definition and excision of neighboring introns in Drosophila. Genes Dev. 28, 1772–1785 (2014).
Malone, C. D. et al. The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript. Genes Dev. 28, 1786–1799 (2014). References 91 and 92 document studies in D. melanogaster showing that depositing EJC proteins at piwi transcripts can enhance the splicing of neighbouring weak introns.
Haremaki, T. & Weinstein, D. C. Eif4a3 is required for accurate splicing of the Xenopus laevis ryanodine receptor pre-mRNA. Dev. Biol. 372, 103–110 (2012).
Michelle, L. et al. Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators. Mol. Cell. Biol. 32, 954–967 (2012).
Wang, Z., Murigneux, V. & Le Hir, H. Transcriptome-wide modulation of splicing by the exon junction complex. Genome Biol. 15, 551 (2014). A genome-wide study showing that fully-assembled EJCs can affect a large number of splicing events, and that EJC effects are linked to Pol II elongation rates.
Crabb, T. L., Lam, B. J. & Hertel, K. J. Retention of spliceosomal components along ligated exons ensures efficient removal of multiple introns. RNA 16, 1786–1796 (2010).
Kornblihtt, A. R. et al. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol. 14, 153–165 (2013).
Huang, Y. & Steitz, J. A. Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA. Mol. Cell 7, 899–905 (2001).
Gatfield, D. & Izaurralde, E. REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export. J. Cell Biol. 159, 579–588 (2002).
Nott, A., Meislin, S. H. & Moore, M. J. A quantitative analysis of intron effects on mammalian gene expression. RNA 9, 607–617 (2003).
Kugler, J. M. & Lasko, P. Localization, anchoring and translational control of oskar, gurken, bicoid and nanos mRNA during Drosophila oogenesis. Fly 3, 15–28 (2009).
Ghosh, S., Marchand, V., Gaspar, I. & Ephrussi, A. Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA. Nat. Struct. Mol. Biol. 19, 441–449 (2012).
Le Hir, H. & Seraphin, B. EJCs at the heart of translational control. Cell 133, 213–216 (2008).
Callis, J., Fromm, M. & Walbot, V. Introns increase gene expression in cultured maize cells. Genes Dev. 1, 1183–1200 (1987).
Hinnebusch, A. G. The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779–812 (2014).
Somers, J., Poyry, T. & Willis, A. E. A perspective on mammalian upstream open reading frame function. Int. J. Biochem. Cell Biol. 45, 1690–1700 (2013).
Le Hir, H., Moore, M. J. & Maquat, L. E. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon–exon junctions. Genes Dev. 14, 1098–1108 (2000).
Yamashita, A. et al. SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. Genes Dev. 23, 1091–1105 (2009).
Hug, N. & Caceres, J. F. The RNA helicase DHX34 activates NMD by promoting a transition from the surveillance to the decay-inducing complex. Cell Rep. 8, 1845–1856 (2014).
Kurosaki, T. et al. A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes Dev. 28, 1900–1916 (2014).
Isken, O. et al. Upf1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay. Cell 133, 314–327 (2008).
Okada-Katsuhata, Y. et al. N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD. Nucleic Acids Res. 40, 1251–1266 (2012).
Chan, W. K. et al. An alternative branch of the nonsense-mediated decay pathway. EMBO J. 26, 1820–1830 (2007).
Chakrabarti, S. et al. Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2. Mol. Cell 41, 693–703 (2011).
Fiorini, F., Boudvillain, M. & Le Hir, H. Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains. Nucleic Acids Res. 41, 2404–2415 (2013).
Franks, T. M., Singh, G. & Lykke-Andersen, J. Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay. Cell 143, 938–950 (2010).
Fiorini, F., Bagchi, D., Le Hir, H. & Croquette, V. Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities. Nat. Commun. 6, 7581 (2015).
Giorgi, C. et al. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell 130, 179–191 (2007). This study showed that changes in eIF4A3 levels cause changes in several neuronal-specific mRNAs, some of which are regulated by EJC-dependent translational decay.
Amrani, N. et al. A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432, 112–118 (2004).
Brogna, S. & Wen, J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nat. Struct. Mol. Biol. 16, 107–113 (2009).
Buhler, M., Steiner, S., Mohn, F., Paillusson, A. & Muhlemann, O. EJC-independent degradation of nonsense immunoglobulin-μ mRNA depends on 3′ UTR length. Nat. Struct. Mol. Biol. 13, 462–464 (2006).
Kerenyi, Z. et al. Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J. 27, 1585–1595 (2008).
Wen, J. & Brogna, S. Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe. EMBO J. 29, 1537–1551 (2010).
Wittkopp, N. et al. Nonsense-mediated mRNA decay effectors are essential for zebrafish embryonic development and survival. Mol. Cell. Biol. 29, 3517–3528 (2009).
Gatfield, D., Unterholzner, L., Ciccarelli, F. D., Bork, P. & Izaurralde, E. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J. 22, 3960–3970 (2003).
Longman, D., Plasterk, R. H., Johnstone, I. L. & Caceres, J. F. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev. 21, 1075–1085 (2007).
Hachet, O. & Ephrussi, A. Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization. Nature 428, 959–963 (2004). This study provided the first evidence that splicing and the EJC are both required for the localization of an mRNA, and implied the potential differential occupancy of EJCs.
Sauliere, J. et al. The exon junction complex differentially marks spliced junctions. Nat. Struct. Mol. Biol. 17, 1269–1271 (2010).
Muhlemann, O. Intimate liaison with SR proteins brings exon junction complexes to unexpected places. Nat. Struct. Mol. Biol. 19, 1209–1211 (2012).
Mishler, D. M., Christ, A. B. & Steitz, J. A. Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate. RNA 14, 2657–2670 (2008).
Huang, Y. & Steitz, J. A. SRprises along a messenger's journey. Mol. Cell 17, 613–615 (2005).
Zhang, Z. & Krainer, A. R. Involvement of SR proteins in mRNA surveillance. Mol. Cell 16, 597–607 (2004).
Sato, H., Hosoda, N. & Maquat, L. E. Efficiency of the pioneer round of translation affects the cellular site of nonsense-mediated mRNA decay. Mol. Cell 29, 255–262 (2008).
Michlewski, G., Sanford, J. R. & Caceres, J. F. The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol. Cell 30, 179–189 (2008).
Gudikote, J. P., Imam, J. S., Garcia, R. F. & Wilkinson, M. F. RNA splicing promotes translation and RNA surveillance. Nat. Struct. Mol. Biol. 12, 801–809 (2005).
Viegas, M. H., Gehring, N. H., Breit, S., Hentze, M. W. & Kulozik, A. E. The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway. Nucleic Acids Res. 35, 4542–4551 (2007).
Zetoune, A. B. et al. Comparison of nonsense-mediated mRNA decay efficiency in various murine tissues. BMC Genet. 9, 83 (2008).
Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009).
Baltz, A. G. et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 46, 674–690 (2012).
Castello, A. et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149, 1393–1406 (2012).
Silver, D. L. et al. The exon junction complex component Magoh controls brain size by regulating neural stem cell division. Nat. Neurosci. 13, 551–558 (2010).
Boswell, R. E., Prout, M. E. & Steichen, J. C. Mutations in a newly identified Drosophila melanogaster gene, mago nashi, disrupt germ cell formation and result in the formation of mirror-image symmetrical double abdomen embryos. Development 113, 373–384 (1991).
Parma, D. H., Bennett, P. E. Jr & Boswell, R. E. Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification. Dev. Biol. 308, 507–519 (2007).
Lewandowski, J. P., Sheehan, K. B., Bennett, P. E. Jr & Boswell, R. E. Mago Nashi, Tsunagi/Y14, and Ranshi form a complex that influences oocyte differentiation in Drosophila melanogaster. Dev. Biol. 339, 307–319 (2010).
van der Weele, C. M., Tsai, C. W. & Wolniak, S. M. Mago nashi is essential for spermatogenesis in Marsilea. Mol. Biol. Cell 18, 3711–3722 (2007).
Boothby, T. C. & Wolniak, S. M. Masked mRNA is stored with aggregated nuclear speckles and its asymmetric redistribution requires a homolog of Mago nashi. BMC Cell Biol. 12, 45 (2011).
Kawano, T., Kataoka, N., Dreyfuss, G. & Sakamoto, H. Ce-Y14 and MAG-1, components of the exon–exon junction complex, are required for embryogenesis and germline sexual switching in Caenorhabditis elegans. Mech. Dev. 121, 27–35 (2004).
Inaki, M. et al. Genetic analyses using a mouse cell cycle mutant identifies magoh as a novel gene involved in Cdk regulation. Genes Cells 16, 166–178 (2011).
Mao, H. et al. Rbm8a haploinsufficiency disrupts embryonic cortical development resulting in microcephaly. J. Neurosci. 35, 7003–7018 (2015).
Silver, D. L., Leeds, K. E., Hwang, H. W., Miller, E. E. & Pavan, W. J. The EJC component Magoh regulates proliferation and expansion of neural crest-derived melanocytes. Dev. Biol. 375, 172–181 (2013).
Haremaki, T., Sridharan, J., Dvora, S. & Weinstein, D. C. Regulation of vertebrate embryogenesis by the exon junction complex core component Eif4a3. Dev. Dyn. 239, 1977–1987 (2010).
Barker-Haliski, M. L., Pastuzyn, E. D. & Keefe, K. A. Expression of the core exon-junction complex factor eukaryotic initiation factor 4A3 is increased during spatial exploration and striatally-mediated learning. Neuroscience 226, 51–61 (2012).
Alachkar, A. et al. An EJC factor RBM8a regulates anxiety behaviors. Curr. Mol. Med. 13, 887–899 (2013).
Nguyen, L. S. et al. Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders. Hum. Mol. Genet. 22, 1816–1825 (2013).
Albers, C. A. et al. Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat. Genet. 44, 435–439 (2012). The first study to link mutations in Y14 to a human disease. In this case, Y14 expression is reduced in platelets, causing TAR syndrome.
Favaro, F. P. et al. A noncoding expansion in EIF4A3 causes Richieri-Costa-Pereira syndrome, a craniofacial disorder associated with limb defects. Am. J. Hum. Genet. 94, 120–128 (2014).
Chan, C. C. et al. eIF4A3 is a novel component of the exon junction complex. RNA 10, 200–209 (2004).
Ferraiuolo, M. A. et al. A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc. Natl Acad. Sci. USA 101, 4118–4123 (2004).
Palacios, I. M., Gatfield, D., St Johnston, D. & Izaurralde, E. An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427, 753–757 (2004).
Alexandrov, A., Colognori, D. & Steitz, J. A. Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex. Genes Dev. 25, 1078–1090 (2011).
Budiman, M. E. et al. Eukaryotic initiation factor 4a3 is a selenium-regulated RNA-binding protein that selectively inhibits selenocysteine incorporation. Mol. Cell 35, 479–489 (2009).
Zhao, X. F., Nowak, N. J., Shows, T. B. & Aplan, P. D. MAGOH interacts with a novel RNA-binding protein. Genomics 63, 145–148 (2000).
Hachet, O. & Ephrussi, A. Drosophila Y14 shuttles to the posterior of the oocyte and is required for oskar mRNA transport. Curr. Biol. 11, 1666–1674 (2001).
Mohr, S. E., Dillon, S. T. & Boswell, R. E. The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis. Genes Dev. 15, 2886–2899 (2001).
Kataoka, N., Diem, M. D., Kim, V. N., Yong, J. & Dreyfuss, G. Magoh, a human homolog of Drosophila mago nashi protein, is a component of the splicing-dependent exon–exon junction complex. EMBO J. 20, 6424–6433 (2001).
Le Hir, H., Gatfield, D., Braun, I. C., Forler, D. & Izaurralde, E. The protein Mago provides a link between splicing and mRNA localization. EMBO Rep. 2, 1119–1124 (2001).
Baguet, A. et al. The exon-junction-complex-component metastatic lymph node 51 functions in stress-granule assembly. J. Cell Sci. 120, 2774–2784 (2007).
Mayeda, A. et al. Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO J. 18, 4560–4570 (1999).
Singh, G., Jakob, S., Kleedehn, M. G. & Lykke-Andersen, J. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. Mol. Cell 27, 780–792 (2007).
Sahara, S. et al. Acinus is a caspase-3-activated protein required for apoptotic chromatin condensation. Nature 401, 168–173 (1999).
Li, C., Lin, R. I., Lai, M. C., Ouyang, P. & Tarn, W. Y. Nuclear Pnn/DRS protein binds to spliced mRNPs and participates in mRNA processing and export via interaction with RNPS1. Mol. Cell. Biol. 23, 7363–7376 (2003).
Rodrigues, J. P. et al. REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus. Proc. Natl Acad. Sci. USA 98, 1030–1035 (2001).
Zhou, Z. et al. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 407, 401–405 (2000).
Gatfield, D. et al. The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila. Curr. Biol. 11, 1716–1721 (2001).
Braun, I. C., Herold, A., Rode, M., Conti, E. & Izaurralde, E. Overexpression of TAP/p15 heterodimers bypasses nuclear retention and stimulates nuclear mRNA export. J. Biol. Chem. 276, 20536–20543 (2001).
Fribourg, S., Braun, I. C., Izaurralde, E. & Conti, E. Structural basis for the recognition of a nucleoporin FG repeat by the NTF2-like domain of the TAP/p15 mRNA nuclear export factor. Mol. Cell 8, 645–656 (2001).
Chan, W. K. et al. A UPF3-mediated regulatory switch that maintains RNA surveillance. Nat. Struct. Mol. Biol. 16, 747–753 (2009).
Kadlec, J., Izaurralde, E. & Cusack, S. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat. Struct. Mol. Biol. 11, 330–337 (2004).
Kadlec, J., Guilligay, D., Ravelli, R. B. & Cusack, S. Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1. RNA 12, 1817–1824 (2006).
Unterholzner, L. & Izaurralde, E. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol. Cell 16, 587–596 (2004).
Research in the authors' laboratory was supported in part by the Centre National de la Recherche Scientifique and the Institut National de la Santé et de la Recherche Médicale, the Agence Nationale de la Recherche (2011-BLAN-BSV8-01801; 2013-BLAN-BSV8-0023; ANR-14-CE10-0014) and the Labex Memolife.
The authors declare no competing financial interests.
A protein domain of the conserved amino-acid sequence DEAD (Asp-Glu-Ala-Asp).
Middle domain of eukaryotic initiation factor 4G (eIF4G). This domain is rich in α-helices and can bind to eIF4A and eIF3E within the eIF4F complex.
- SR proteins
A conserved protein family involved mainly in RNA splicing. SR proteins contain domains with long repeats of Ser (S) and Arg (R) at the carboxyl terminus, which gives their name. They also contain at least one RRM (RNA-recognition motif) at their amino terminus.
- Ribosome scanning
During cap-dependent translation initiation, the 40S small ribosomal unit, together with the tRNA, forms the 43S pre-initiation complex, which 'scans' the mRNA towards the 3′ end from the start codon.
Group of proteins involved in transporting molecules between the cytoplasm and the nucleus through nuclear pores in eukaryotes.
- Weak intron
An intron that contains suboptimal splice sites compared to consensus sequence, leading to less efficient recognition by the spliceosomes.
- Cassette exons
Exons that are either included or skipped from the precursor mRNA (pre-mRNA), resulting in the formation of different mRNA isoforms.
- Faux 3′ UTR
A model of nonsense-mediated decay (NMD), stating that premature translation termination is inefficient because the terminating ribosomes are far from the poly(A)-binding proteins present at the poly(A) tail, and thus the ribosomes interact instead with up frameshift (UPF) proteins, resulting in NMD.
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Hir, H., Saulière, J. & Wang, Z. The exon junction complex as a node of post-transcriptional networks. Nat Rev Mol Cell Biol 17, 41–54 (2016). https://doi.org/10.1038/nrm.2015.7
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