Exon Junction Complexes: Supervising the Gene Expression Assembly Line

Le Hir, 2016, The exon junction complex as a node of post-transcriptional networks, Nat. Rev. Mol. Cell Biol., 17, 41, 10.1038/nrm.2015.7

Lykke-Andersen, 2001, Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1, Science, 293, 1836, 10.1126/science.1062786

Le Hir, 2001, The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay, EMBO J., 20, 4987, 10.1093/emboj/20.17.4987

Kim, 2001, Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex, Science, 293, 1832, 10.1126/science.1062829

Cheng, 1994, Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance, Mol. Cell. Biol., 14, 6317, 10.1128/MCB.14.9.6317

Kugler, 1995, Nuclear degradation of nonsense mutated beta-globin mRNA: a post-transcriptional mechanism to protect heterozygotes from severe clinical manifestations of beta-thalassemia?, Nucleic Acids Res., 23, 413, 10.1093/nar/23.3.413

Carter, 1996, A splicing-dependent regulatory mechanism that detects translation signals, EMBO J., 15, 5965, 10.1002/j.1460-2075.1996.tb00983.x

Thermann, 1998, Binary specification of nonsense codons by splicing and cytoplasmic translation, EMBO J., 17, 3484, 10.1093/emboj/17.12.3484

Le Hir, 2000, The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions, EMBO J., 19, 6860, 10.1093/emboj/19.24.6860

Le Hir, 2000, Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions, Genes Dev., 14, 1098, 10.1101/gad.14.9.1098

Kataoka, 2000, Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm, Mol. Cell, 6, 673, 10.1016/S1097-2765(00)00065-4

Ferraiuolo, 2004, A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay, Proc. Natl. Acad. Sci. U.S.A., 101, 4118, 10.1073/pnas.0400933101

Palacios, 2004, An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay, Nature, 427, 753, 10.1038/nature02351

Shibuya, 2004, eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay, Nat. Struct. Mol. Biol., 11, 346, 10.1038/nsmb750

Tange, 2005, Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core, RNA, 11, 1869, 10.1261/rna.2155905

Chan, 2004, eIF4A3 is a novel component of the exon junction complex, RNA, 10, 200, 10.1261/rna.5230104

Andersen, 2006, Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA, Science, 313, 1968, 10.1126/science.1131981

Bono, 2006, The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA, Cell, 126, 713, 10.1016/j.cell.2006.08.006

Ballut, 2005, The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity, Nat. Struct. Mol. Biol., 12, 861, 10.1038/nsmb990

Wahl, 2009, The spliceosome: design principles of a dynamic RNP machine, Cell, 136, 701, 10.1016/j.cell.2009.02.009

Gehring, 2009, The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay, PLoS Biol., 7, e1000120, 10.1371/journal.pbio.1000120

Alexandrov, 2012, Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay, Proc. Natl. Acad. Sci. U.S.A., 109, 21313, 10.1073/pnas.1219725110

Barbosa, 2012, Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes exon junction complex assembly, Nat. Struct. Mol. Biol., 19, 983, 10.1038/nsmb.2380

Steckelberg, 2012, CWC22 connects pre-mRNA splicing and exon junction complex assembly, Cell Rep., 2, 454, 10.1016/j.celrep.2012.08.017

Steckelberg, 2015, CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes, Nucleic Acids Res., 43, 4687, 10.1093/nar/gkv320

Bessonov, 2008, Isolation of an active step I spliceosome and composition of its RNP core, Nature, 452, 846, 10.1038/nature06842

Buchwald, 2013, Crystal structure of the human eIF4AIII-CWC22 complex shows how a DEAD-box protein is inhibited by a MIF4G domain, Proc. Natl. Acad. Sci. U.S.A., 110, E4611, 10.1073/pnas.1314684110

Wan, 2016, Structure of a yeast catalytic step I spliceosome at 3.4 A resolution, Science, 353, 895, 10.1126/science.aag2235

Rauhut, 2016, Molecular architecture of the Saccharomyces cerevisiae activated spliceosome, Science, 10.1126/science.aag1906

Galej, 2016, Cryo-EM structure of the spliceosome immediately after branching, Nature, 537, 197, 10.1038/nature19316

Ideue, 2007, Introns play an essential role in splicing-dependent formation of the exon junction complex, Genes Dev., 21, 1993, 10.1101/gad.1557907

Sauliere, 2012, CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex, Nat. Struct. Mol. Biol., 19, 1124, 10.1038/nsmb.2420

Singh, 2012, The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus, Cell, 151, 750, 10.1016/j.cell.2012.10.007

Hauer, 2016, Exon junction complexes show a distributional bias toward alternatively spliced mRNAs and against mRNAs coding for ribosomal proteins, Cell Rep., 16, 1588, 10.1016/j.celrep.2016.06.096

Lee, 2015, Mechanisms and regulation of alternative Pre-mRNA splicing, Annu. Rev. Biochem., 84, 291, 10.1146/annurev-biochem-060614-034316

Long, 2009, The SR protein family of splicing factors: master regulators of gene expression, Biochem. J., 417, 15, 10.1042/BJ20081501

Twyffels, 2011, Shuttling SR proteins: more than splicing factors, FEBS J., 278, 3246, 10.1111/j.1742-4658.2011.08274.x

Dostie, 2002, Translation is required to remove Y14 from mRNAs in the cytoplasm, Curr. Biol., 12, 1060, 10.1016/S0960-9822(02)00902-8

Bono, 2004, Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex, EMBO Rep., 5, 304, 10.1038/sj.embor.7400091

Gehring, 2009, Disassembly of exon junction complexes by PYM, Cell, 137, 536, 10.1016/j.cell.2009.02.042

Diem, 2007, PYM binds the cytoplasmic exon-junction complex and ribosomes to enhance translation of spliced mRNAs, Nat. Struct. Mol. Biol., 14, 1173, 10.1038/nsmb1321

Ghosh, 2014, The EJC binding and dissociating activity of PYM is regulated in Drosophila, PLoS Genet., 10, e1004455, 10.1371/journal.pgen.1004455

Schwerk, 2003, ASAP, a novel protein complex involved in RNA processing and apoptosis, Mol. Cell. Biol., 23, 2981, 10.1128/MCB.23.8.2981-2990.2003

Li, 2003, Nuclear Pnn/DRS protein binds to spliced mRNPs and participates in mRNA processing and export via interaction with RNPS1, Mol. Cell. Biol., 23, 7363, 10.1128/MCB.23.20.7363-7376.2003

Murachelli, 2012, The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex, Nat. Struct. Mol. Biol., 19, 378, 10.1038/nsmb.2242

Schmidt, 2014, Mass spectrometry-based relative quantification of proteins in precatalytic and catalytically active spliceosomes by metabolic labeling (SILAC), chemical labeling (iTRAQ), and label-free spectral count, RNA, 20, 406, 10.1261/rna.041244.113

Singh, 2010, Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold, RNA, 16, 2442, 10.1261/rna.2304410

Mayeda, 1999, Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing, EMBO J., 18, 4560, 10.1093/emboj/18.16.4560

Sakashita, 2004, Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo, Mol. Cell. Biol., 24, 1174, 10.1128/MCB.24.3.1174-1187.2004

Wang, 2015, Role of Acinus in regulating retinoic acid-responsive gene pre-mRNA splicing, J. Cell. Physiol., 230, 791, 10.1002/jcp.24804

Michelle, 2012, Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators, Mol. Cell. Biol., 32, 954, 10.1128/MCB.06130-11

Rodor, 2016, The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation, RNA, 22, 1411, 10.1261/rna.057158.116

Zhang, 2007, Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components, Proc. Natl. Acad. Sci. U.S.A., 104, 11574, 10.1073/pnas.0704946104

Hayashi, 2014, The exon junction complex is required for definition and excision of neighboring introns in Drosophila, Genes Dev., 28, 1772, 10.1101/gad.245738.114

Ashton-Beaucage, 2010, The exon junction complex controls the splicing of MAPK and other long intron-containing transcripts in Drosophila, Cell, 143, 251, 10.1016/j.cell.2010.09.014

Roignant, 2010, Exon junction complex subunits are required to splice Drosophila MAP kinase, a large heterochromatic gene, Cell, 143, 238, 10.1016/j.cell.2010.09.036

Malone, 2014, The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript, Genes Dev., 28, 1786, 10.1101/gad.245829.114

Wang, 2014, Transcriptome-wide modulation of splicing by the exon junction complex, Genome Biol., 15, 551, 10.1186/s13059-014-0551-7

Valencia, 2008, Splicing promotes rapid and efficient mRNA export in mammalian cells, Proc. Natl. Acad. Sci. U.S.A., 105, 3386, 10.1073/pnas.0800250105

Adam, 1986, mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence, Mol. Cell. Biol., 6, 2932, 10.1128/MCB.6.8.2932

Luo, 2001, Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly, Nature, 413, 644, 10.1038/35098106

Zhou, 2000, The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans, Nature, 407, 401, 10.1038/35030160

Strasser, 2002, TREX is a conserved complex coupling transcription with messenger RNA export, Nature, 417, 304, 10.1038/nature746

Viphakone, 2012, TREX exposes the RNA–binding domain of Nxf1 to enable mRNA export, Nat. Commun., 3, 1006, 10.1038/ncomms2005

Hautbergue, 2008, Mutually exclusive interactions drive handover of mRNA from export adaptors to TAP, Proc. Natl. Acad. Sci. U.S.A., 105, 5154, 10.1073/pnas.0709167105

Grunwald, 2011, Nuclear export dynamics of RNA-protein complexes, Nature, 475, 333, 10.1038/nature10318

Besse, 2008, Translational control of localized mRNAs: restricting protein synthesis in space and time, Nat. Rev. Mol. Cell Biol., 9, 971, 10.1038/nrm2548

Ephrussi, 1991, Oskar organizes the germ plasm and directs localization of the posterior determinant nanos, Cell, 66, 37, 10.1016/0092-8674(91)90137-N

Kim-Ha, 1991, oskar mRNA is localized to the posterior pole of the Drosophila oocyte, Cell, 66, 23, 10.1016/0092-8674(91)90136-M

Ghosh, 2012, Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA, Nat. Struct. Mol. Biol., 19, 441, 10.1038/nsmb.2257

Nott, 2003, A quantitative analysis of intron effects on mammalian gene expression, RNA, 9, 607, 10.1261/rna.5250403

Wiegand, 2003, Exon junction complexes mediate the enhancing effect of splicing on mRNA expression, Proc. Natl. Acad. Sci. U.S.A., 100, 11327, 10.1073/pnas.1934877100

Nott, 2004, Splicing enhances translation in mammalian cells: an additional function of the exon junction complex, Genes Dev., 18, 210, 10.1101/gad.1163204

Chazal, 2013, EJC core component MLN51 interacts with eIF3 and activates translation, Proc. Natl. Acad. Sci. U.S.A., 110, 5903, 10.1073/pnas.1218732110

Choe, 2014, eIF4AIII enhances translation of nuclear cap-binding complex-bound mRNAs by promoting disruption of secondary structures in 5′UTR, Proc. Natl. Acad. Sci. U.S.A., 111, E4577, 10.1073/pnas.1409695111

Noble, 2007, MLN51 stimulates the RNA-helicase activity of eIF4AIII, PLoS One, 2, e303, 10.1371/journal.pone.0000303

Ma, 2008, SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs, Cell, 133, 303, 10.1016/j.cell.2008.02.031

Lejeune, 2002, 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, 10.1093/emboj/cdf345

Nagy, 1998, A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance, Trends Biochem. Sci., 23, 19819, 10.1016/S0968-0004(98)01208-0

Lykke-Andersen, 2015, Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes, Nat. Rev. Mol. Cell Biol., 16, 665, 10.1038/nrm4063

Fatscher, 2015, Mechanism, factors, and physiological role of nonsense-mediated mRNA decay, Cell. Mol. Life Sci., 72, 4523, 10.1007/s00018-015-2017-9

Chamieh, 2008, NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity, Nat. Struct. Mol. Biol., 15, 85, 10.1038/nsmb1330

Buchwald, 2010, Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex, Proc. Natl. Acad. Sci. U.S.A., 107, 10050, 10.1073/pnas.1000993107

Gehring, 2003, Y14 and hUpf3b form an NMD-activating complex, Mol. Cell, 11, 939, 10.1016/S1097-2765(03)00142-4

Yamashita, 2013, Role of SMG-1-mediated Upf1 phosphorylation in mammalian nonsense-mediated mRNA decay, Genes Cells, 18, 161, 10.1111/gtc.12033

Eberle, 2009, SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells, Nat. Struct. Mol. Biol., 16, 49, 10.1038/nsmb.1530

Loh, 2013, The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2, Genes Dev., 27, 2125, 10.1101/gad.226951.113

Boehm, 2014, 3′ UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons, Cell Rep., 9, 555, 10.1016/j.celrep.2014.09.012

Albers, 2013, New insights into the genetic basis of TAR (thrombocytopenia-absent radii) syndrome, Curr. Opin. Genet. Dev., 23, 316, 10.1016/j.gde.2013.02.015

Albers, 2012, 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, 10.1038/ng.1083

Rosenfeld, 2012, Proximal microdeletions and microduplications of 1q21.1 contribute to variable abnormal phenotypes, Eur. J. Hum. Genet., 20, 754, 10.1038/ejhg.2012.6

Favaro, 2011, Richieri-Costa-Pereira syndrome: a unique acrofacial dysostosis type. An overview of the Brazilian cases, Am. J. Med. Genet. A, 155A, 322, 10.1002/ajmg.a.33806

Favaro, 2014, A noncoding expansion in EIF4A3 causes Richieri-Costa-Pereira syndrome, a craniofacial disorder associated with limb defects, Am. J. Hum. Genet., 94, 120, 10.1016/j.ajhg.2013.11.020

McMahon, 2016, The exon junction complex in neural development and neurodevelopmental disease, Int. J. Dev. Neurosci., 10.1016/j.ijdevneu.2016.03.006

Silver, 2010, The exon junction complex component Magoh controls brain size by regulating neural stem cell division, Nat. Neurosci., 13, 551, 10.1038/nn.2527

Mao, 2015, Rbm8a haploinsufficiency disrupts embryonic cortical development resulting in microcephaly, J. Neurosci., 35, 7003, 10.1523/JNEUROSCI.0018-15.2015

Zou, 2015, A critical role of RBM8a in proliferation and differentiation of embryonic neural progenitors, Neural Dev., 10, 18, 10.1186/s13064-015-0045-7