The Experts below are selected from a list of 1989 Experts worldwide ranked by ideXlab platform
Hervé Le Hir - One of the best experts on this subject based on the ideXlab platform.
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The Exon Junction Complex as a node of post-transcriptional networks
Nature Reviews Molecular Cell Biology, 2016Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract:In addition to its known roles in nonsense-mediated mRNA decay, recent findings show that the Exon Junction Complex (EJC) participates in diverse mRNA maturation processes, including splicing, transport and translation. This multi-functionality is reflected by an increasing number of EJC-related disorders being discovered. 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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The Exon Junction Complex as a node of post-transcriptional networks.
Nature reviews. Molecular cell biology, 2015Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract: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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The Exon Junction Complex as a node of post-transcriptional networks.
Nature reviews. Molecular cell biology, 2015Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract:In addition to its known roles in nonsense-mediated mRNA decay, recent findings show that the Exon Junction Complex (EJC) participates in diverse mRNA maturation processes, including splicing, transport and translation. This multi-functionality is reflected by an increasing number of EJC-related disorders being discovered. 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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Transcriptome-wide modulation of splicing by the Exon Junction Complex
Genome Biology, 2014Co-Authors: Zhen Wang, Valentine Murigneux, Hervé Le HirAbstract:Background The Exon Junction Complex (EJC) is a dynamic multi-protein Complex deposited onto nuclear spliced mRNAs upstream of Exon-Exon Junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells. Results Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates. Conclusion Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition.
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Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes Exon Junction Complex assembly
Nature structural & molecular biology, 2012Co-Authors: Isabelle Barbosa, Charlotte Barrandon, Francesca Fiorini, Marco Blanchette, Nazmul Haque, Catherine Tomasetto, Hervé Le HirAbstract:The Exon Junction Complex (EJC) links splicing to downstream events including mRNA localization, translation and stability. A combination of in vitro and in vivo approaches were used to identify the splicing factor CWC22 as a direct partner of EJC component eIF4AIII in flies and humans and to demonstrate its functions in preventing eIF4AIII binding to RNA and in escorting eIF4AIII to active spliceosomes before EJC assembly.
Gideon Dreyfuss - One of the best experts on this subject based on the ideXlab platform.
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PYM binds the cytoplasmic Exon-Junction Complex and ribosomes to enhance translation of spliced mRNAs
Nature structural & molecular biology, 2007Co-Authors: Michael D. Diem, Chia C. Chan, Ihab Younis, Gideon DreyfussAbstract:Messenger RNAs produced by splicing are translated more efficiently than those produced from similar intronless precursor mRNAs (pre-mRNAs). The Exon-Junction Complex (EJC) probably mediates this enhancement; however, the specific link between the EJC and the translation machinery has not been identified. The EJC proteins Y14 and magoh remain bound to spliced mRNAs after their export from the nucleus to the cytoplasm and are removed only when these mRNAs are translated. Here we show that PYM, a 29-kDa protein that binds the Y14-magoh Complex in the cytoplasm, also binds, via a separate domain, to the small (40S) ribosomal subunit and the 48S preinitiation Complex. Furthermore, PYM knockdown reduces the translation efficiency of a reporter protein produced from intron-containing, but not intronless, pre-mRNA. We suggest that PYM functions as a bridge between EJC-bearing spliced mRNAs and the translation machinery to enhance translation of the mRNAs.
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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 & development, 2006Co-Authors: Gideon Dreyfuss, Isao Kashima, Naoyuki Kataoka, Akio Yamashita, Natsuko Izumi, Ryo Morishita, Shinichi Hoshino, Mutsuhito Ohno, Shigeo OhnoAbstract:Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNA containing premature termination codons (PTCs). In mammalian cells, recognition of PTCs requires translation and depends on the presence on the mRNA with the splicing-dependent Exon Junction Complex (EJC). While it is known that a key event in the triggering of NMD is phosphorylation of the trans-acting factor, Upf1, by SMG-1, the relationship between Upf1 phosphorylation and PTC recognition remains undetermined. Here we show that SMG-1 binds to the mRNA-associated components of the EJC, Upf2, Upf3b, eIF4A3, Magoh, and Y14. Further, we describe a novel Complex that contains the NMD factors SMG-1 and Upf1, and the translation termination release factors eRF1 and eRF3 (SURF). Importantly, an association between SURF and the EJC is required for SMG-1-mediated Upf1 phosphorylation and NMD. Thus, the SMG-1-mediated phosphorylation of Upf1 occurs on the association of SURF with EJC, which provides the link between the EJC and recognition of PTCs and triggers NMD.
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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 & Development, 2006Co-Authors: Gideon Dreyfuss, Isao Kashima, Naoyuki Kataoka, Akio Yamashita, Natsuko Izumi, Ryo Morishita, Shinichi Hoshino, Mutsuhito Ohno, Shigeo OhnoAbstract:Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNA containing premature termination codons (PTCs). In mammalian cells, recognition of PTCs requires translation and depends on the presence on the mRNA with the splicing-dependent Exon Junction Complex (EJC). While it is known that a key event in the triggering of NMD is phosphorylation of the trans-acting factor, Upf1, by SMG-1, the relationship between Upf1 phosphorylation and PTC recognition remains undetermined. Here we show that SMG-1 binds to the mRNA-associated components of the EJC, Upf2, Upf3b, eIF4A3, Magoh, and Y14. Further, we describe a novel Complex that contains the NMD factors SMG-1 and Upf1, and the translation termination release factors eRF1 and eRF3 (SURF). Importantly, an association between SURF and the EJC is required for SMG-1-mediated Upf1 phosphorylation and NMD. Thus, the SMG-1-mediated phosphorylation of Upf1 occurs on the association of SURF with EJC, which provides the link between the EJC and recognition of PTCs and triggers NMD.
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eIF4A3 is a novel component of the Exon Junction Complex
Rna, 2004Co-Authors: Chia C. Chan, Michael D. Diem, Wenqin Feng, Josee Dostie, Matthias Mann, Juri Rappsilber, Gideon DreyfussAbstract:The Exon Junction Complex (EJC) is a protein Complex that assembles near Exon–Exon Junctions of mRNAs as a result of splicing. EJC proteins play important roles in postsplicing events including mRNA export, cytoplasmic localization, and nonsense-mediated decay. Recent evidence suggests that mRNA translation is also influenced by the splicing history of the transcript. Here we identify eIF4A3, a DEAD-box RNA helicase and a member of the eIF4A family of translation initiation factors, as a novel component of the EJC. We show that eIF4A3 associates preferentially with nuclear Complexes containing the EJC proteins magoh and Y14. Furthermore, eIF4A3, but not the highly related eIF4A1 or eIF4A2, preferentially associates with spliced mRNA. In vitro splicing and mapping experiments demonstrate that eIF4A3 binds mRNAs at the position of the EJC. Using monoclonal antibodies, we show that eIF4A3 is found in the nucleus whereas eIF4A1 and eIF4A2 are found in the cytoplasm. Thus, eIF4A3 likely provides a splicing-dependent influence on the translation of mRNAs.
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Ce-Y14 and MAG-1, components of the Exon-Exon Junction Complex, are required for embryogenesis and germline sexual switching in Caenorhabditis elegans.
Mechanisms of development, 2004Co-Authors: Taizo Kawano, Gideon Dreyfuss, Naoyuki Kataoka, Hiroshi SakamotoAbstract:Y14 is a component of the splicing-dependent Exon-Exon Junction Complex (EJC) and is involved in the mRNA quality control system called nonsense-mediated mRNA decay. It has recently been shown that together with another EJC component, Mago, the Drosophila homologue DmY14/Tsunagi is required for proper localization of oskar mRNA during oogenesis, a process critical for posterior formation in Drosophila development. Here we show that the nematode Caenorhabditis elegans Ce-Y14 and MAG-1 (Mago homologue) are required for late embryogenesis and proper germline sexual differentiation. Like in other organisms, Ce-Y14 preferentially binds to spliced mRNA and specifically interacts with MAG-1. Consistent with the evolutionarily conserved interaction between Y14 and Mago homologues, suppression of Ce-Y14 by RNAi resulted in the same phenotypes as those caused by RNAi of mag-1 lethality during late embryogenesis and masculinization of the adult hermaphrodite germline. Our results demonstrate that the evolutionarily conserved interaction between two EJC components, Ce-Y14 and MAG-1, has critical developmental roles in C. elegans.
Naoyuki Kataoka - One of the best experts on this subject based on the ideXlab platform.
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The Exon Junction Complex Controls the Efficient and Faithful Splicing of a Subset of Transcripts Involved in Mitotic Cell-Cycle Progression
International journal of molecular sciences, 2016Co-Authors: Kazuhiro Fukumura, Shunichi Wakabayashi, Naoyuki Kataoka, Hiroshi Sakamoto, Yutaka Suzuki, Kenta Nakai, Akila Mayeda, Kunio InoueAbstract:The Exon Junction Complex (EJC) that is deposited onto spliced mRNAs upstream of Exon–Exon Junctions plays important roles in multiple post-splicing gene expression events, such as mRNA export, surveillance, localization, and translation. However, a direct role for the human EJC in pre-mRNA splicing has not been fully understood. Using HeLa cells, we depleted one of the EJC core components, Y14, and the resulting transcriptome was analyzed by deep sequencing (RNA-Seq) and confirmed by RT–PCR. We found that Y14 is required for efficient and faithful splicing of a group of transcripts that is enriched in short intron-containing genes involved in mitotic cell-cycle progression. Tethering of EJC core components (Y14, eIF4AIII or MAGOH) to a model reporter pre-mRNA harboring a short intron showed that these core components are prerequisites for the splicing activation. Taken together, we conclude that the EJC core assembled on pre-mRNA is critical for efficient and faithful splicing of a specific subset of short introns in mitotic cell cycle-related genes.
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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 & development, 2006Co-Authors: Gideon Dreyfuss, Isao Kashima, Naoyuki Kataoka, Akio Yamashita, Natsuko Izumi, Ryo Morishita, Shinichi Hoshino, Mutsuhito Ohno, Shigeo OhnoAbstract:Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNA containing premature termination codons (PTCs). In mammalian cells, recognition of PTCs requires translation and depends on the presence on the mRNA with the splicing-dependent Exon Junction Complex (EJC). While it is known that a key event in the triggering of NMD is phosphorylation of the trans-acting factor, Upf1, by SMG-1, the relationship between Upf1 phosphorylation and PTC recognition remains undetermined. Here we show that SMG-1 binds to the mRNA-associated components of the EJC, Upf2, Upf3b, eIF4A3, Magoh, and Y14. Further, we describe a novel Complex that contains the NMD factors SMG-1 and Upf1, and the translation termination release factors eRF1 and eRF3 (SURF). Importantly, an association between SURF and the EJC is required for SMG-1-mediated Upf1 phosphorylation and NMD. Thus, the SMG-1-mediated phosphorylation of Upf1 occurs on the association of SURF with EJC, which provides the link between the EJC and recognition of PTCs and triggers NMD.
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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 & Development, 2006Co-Authors: Gideon Dreyfuss, Isao Kashima, Naoyuki Kataoka, Akio Yamashita, Natsuko Izumi, Ryo Morishita, Shinichi Hoshino, Mutsuhito Ohno, Shigeo OhnoAbstract:Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNA containing premature termination codons (PTCs). In mammalian cells, recognition of PTCs requires translation and depends on the presence on the mRNA with the splicing-dependent Exon Junction Complex (EJC). While it is known that a key event in the triggering of NMD is phosphorylation of the trans-acting factor, Upf1, by SMG-1, the relationship between Upf1 phosphorylation and PTC recognition remains undetermined. Here we show that SMG-1 binds to the mRNA-associated components of the EJC, Upf2, Upf3b, eIF4A3, Magoh, and Y14. Further, we describe a novel Complex that contains the NMD factors SMG-1 and Upf1, and the translation termination release factors eRF1 and eRF3 (SURF). Importantly, an association between SURF and the EJC is required for SMG-1-mediated Upf1 phosphorylation and NMD. Thus, the SMG-1-mediated phosphorylation of Upf1 occurs on the association of SURF with EJC, which provides the link between the EJC and recognition of PTCs and triggers NMD.
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Ce-Y14 and MAG-1, components of the Exon-Exon Junction Complex, are required for embryogenesis and germline sexual switching in Caenorhabditis elegans.
Mechanisms of development, 2004Co-Authors: Taizo Kawano, Gideon Dreyfuss, Naoyuki Kataoka, Hiroshi SakamotoAbstract:Y14 is a component of the splicing-dependent Exon-Exon Junction Complex (EJC) and is involved in the mRNA quality control system called nonsense-mediated mRNA decay. It has recently been shown that together with another EJC component, Mago, the Drosophila homologue DmY14/Tsunagi is required for proper localization of oskar mRNA during oogenesis, a process critical for posterior formation in Drosophila development. Here we show that the nematode Caenorhabditis elegans Ce-Y14 and MAG-1 (Mago homologue) are required for late embryogenesis and proper germline sexual differentiation. Like in other organisms, Ce-Y14 preferentially binds to spliced mRNA and specifically interacts with MAG-1. Consistent with the evolutionarily conserved interaction between Y14 and Mago homologues, suppression of Ce-Y14 by RNAi resulted in the same phenotypes as those caused by RNAi of mag-1 lethality during late embryogenesis and masculinization of the adult hermaphrodite germline. Our results demonstrate that the evolutionarily conserved interaction between two EJC components, Ce-Y14 and MAG-1, has critical developmental roles in C. elegans.
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A simple whole cell lysate system for in vitro splicing reveals a stepwise assembly of the Exon-Exon Junction Complex
The Journal of biological chemistry, 2003Co-Authors: Gideon Dreyfuss, Naoyuki KataokaAbstract:Pre-mRNA splicing removes introns and leaves in its wake a multiprotein Complex near the Exon-Exon Junctions of mRNAs. This Complex, termed the Exon-Exon Junction Complex (EJC), contains at least seven proteins and provides a link between pre-mRNA splicing and downstream events, including transport, localization, and nonsense-mediated mRNA decay. Using a simple whole cell lysate system we developed for in vitro splicing, we prepared lysates from cells transfected with tagged EJC proteins and studied the association of these proteins with pre-mRNA, splicing intermediates, and mRNA, as well as formation of the EJC during splicing. Three of the EJC components, Aly/REF, RNPS1, and SRm160, are found on pre-mRNA by the time the spliceosome is formed, whereas Upf3b associates with splicing intermediates during or immediately after the first catalytic step of the splicing reaction (cleavage of Exon 1 and intron-lariat formation). In contrast, Y14 and magoh, which remain stably associated with mRNA after export to the cytoplasm, join the EJC during or after completion of Exon-Exon ligation. These findings indicate that EJC formation is an ordered pathway that involves stepwise association of components and is coupled to specific intermediates of the splicing reaction.
Zhen Wang - One of the best experts on this subject based on the ideXlab platform.
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The Exon Junction Complex as a node of post-transcriptional networks
Nature Reviews Molecular Cell Biology, 2016Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract:In addition to its known roles in nonsense-mediated mRNA decay, recent findings show that the Exon Junction Complex (EJC) participates in diverse mRNA maturation processes, including splicing, transport and translation. This multi-functionality is reflected by an increasing number of EJC-related disorders being discovered. 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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The Exon Junction Complex as a node of post-transcriptional networks.
Nature reviews. Molecular cell biology, 2015Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract: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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The Exon Junction Complex as a node of post-transcriptional networks.
Nature reviews. Molecular cell biology, 2015Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract:In addition to its known roles in nonsense-mediated mRNA decay, recent findings show that the Exon Junction Complex (EJC) participates in diverse mRNA maturation processes, including splicing, transport and translation. This multi-functionality is reflected by an increasing number of EJC-related disorders being discovered. 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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Transcriptome-wide modulation of splicing by the Exon Junction Complex
Genome Biology, 2014Co-Authors: Zhen Wang, Valentine MurigneuxAbstract:Background The Exon Junction Complex (EJC) is a dynamic multi-protein Complex deposited onto nuclear spliced mRNAs upstream of Exon-Exon Junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells. Results Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates. Conclusion Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition.
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Transcriptome-wide modulation of splicing by the Exon Junction Complex
Genome Biology, 2014Co-Authors: Zhen Wang, Valentine Murigneux, Hervé Le HirAbstract:Background The Exon Junction Complex (EJC) is a dynamic multi-protein Complex deposited onto nuclear spliced mRNAs upstream of Exon-Exon Junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells. Results Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates. Conclusion Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition.
Jérôme Saulière - One of the best experts on this subject based on the ideXlab platform.
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The Exon Junction Complex as a node of post-transcriptional networks
Nature Reviews Molecular Cell Biology, 2016Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract:In addition to its known roles in nonsense-mediated mRNA decay, recent findings show that the Exon Junction Complex (EJC) participates in diverse mRNA maturation processes, including splicing, transport and translation. This multi-functionality is reflected by an increasing number of EJC-related disorders being discovered. 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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The Exon Junction Complex as a node of post-transcriptional networks.
Nature reviews. Molecular cell biology, 2015Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract: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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The Exon Junction Complex as a node of post-transcriptional networks.
Nature reviews. Molecular cell biology, 2015Co-Authors: Hervé Le Hir, Jérôme Saulière, Zhen WangAbstract:In addition to its known roles in nonsense-mediated mRNA decay, recent findings show that the Exon Junction Complex (EJC) participates in diverse mRNA maturation processes, including splicing, transport and translation. This multi-functionality is reflected by an increasing number of EJC-related disorders being discovered. 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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CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human Exon Junction Complex
Nature Structural & Molecular Biology, 2012Co-Authors: Jérôme Saulière, Emélie Marquenet, Isabelle Barbosa, Olivier Le Tonquèze, Luc Paillard, Valentine Murigneux, Yann Audic, Zhen Wang, Hugues Roest CrolliusAbstract: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. The Exon Junction Complex (EJC) has a crucial role in various post-transcriptional control mechanisms. CLIP-Seq analysis of the human EJC component eIF4AIII has revealed peaks in canonical EJC-binding regions, including ~24 nucleotides upstream of Exon Junctions. Surprisingly, EJCs are also present elsewhere in the transcriptome, uncovering an unexpected heterogeneity of EJC association with mRNAs.
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CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human Exon Junction Complex
Nature Structural and Molecular Biology, 2012Co-Authors: Jérôme Saulière, Emélie Marquenet, Isabelle Barbosa, Olivier Le Tonquèze, Luc Paillard, Hugues Roest Crollius, Valentine Murigneux, Yann Audic, Zhen Wang, Hervé Le HirAbstract: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.