51
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Boehm V, Gehring NH. Exon Junction Complexes: Supervising the Gene Expression Assembly Line. Trends Genet 2016; 32:724-735. [PMID: 27667727 DOI: 10.1016/j.tig.2016.09.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/23/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
The exon junction complex (EJC) is an RNA-binding protein complex that is assembled and deposited onto mRNAs during splicing. The EJC comprises four core components that bind to not only canonical sites upstream of exon-exon junctions, but also to noncanonical sites at other positions in exons. EJC-associated proteins are recruited by the EJC at different steps of gene expression to execute the multiple functions of the EJC. Recently, new insights have been obtained into how EJCs stimulate pre-mRNA splicing, and mRNA export, translation, and degradation. Furthermore, mutations in EJC core components were shown to result in severe disorders in humans, demonstrating the critical physiological role of the EJC. Hence, the EJC has been identified as an important player in post-transcriptional gene regulation in metazoans.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
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52
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Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M. Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution. Nucleic Acids Res 2016; 45:938-950. [PMID: 27604873 PMCID: PMC5314787 DOI: 10.1093/nar/gkw792] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/22/2016] [Accepted: 08/28/2016] [Indexed: 12/11/2022] Open
Abstract
Our current knowledge about the mechanisms of miRNA silencing is restricted to few lineages such as vertebrates, arthropods, nematodes and land plants. miRNA-mediated silencing in bilaterian animals is dependent on the proteins of the GW182 family. Here, we dissect the function of GW182 protein in the cnidarian Nematostella, separated by 600 million years from other Metazoa. Using cultured human cells, we show that Nematostella GW182 recruits the CCR4-NOT deadenylation complexes via its tryptophan-containing motifs, thereby inhibiting translation and promoting mRNA decay. Further, similarly to bilaterians, GW182 in Nematostella is recruited to the miRNA repression complex via interaction with Argonaute proteins, and functions downstream to repress mRNA. Thus, our work suggests that this mechanism of miRNA-mediated silencing was already active in the last common ancestor of Cnidaria and Bilateria.
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Affiliation(s)
- Marta Mauri
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Marieluise Kirchner
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Reuven Aharoni
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Camilla Ciolli Mattioli
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - David van den Bruck
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Nadya Gutkovitch
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Matthias Selbach
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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53
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Tatsuno T, Nakamura Y, Ma S, Tomosugi N, Ishigaki Y. Nonsense-mediated mRNA decay factor Upf2 exists in both the nucleoplasm and the cytoplasm. Mol Med Rep 2016; 14:655-60. [PMID: 27221324 PMCID: PMC4918542 DOI: 10.3892/mmr.2016.5331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 04/20/2016] [Indexed: 11/24/2022] Open
Abstract
Upf2 protein predominantly localizes to the cytoplasmic fraction, and binds to the exon junction complex (EJC) on spliced mRNA. The present study aimed to determine the cellular site where the interaction between Upf2 and EJC occurs. First, the cell lysate was fractionated into the cytoplasm and nucleoplasm, and western blotting to detect levels of Upf2 protein was performed. Upf2 was clearly detected in the cytoplasm and in the nucleoplasm. Secondly, immunostaining was performed, and the majority of Upf2 was detected in the cytoplasmic perinuclear region; a small quantity of Upf2 was detected in the intranuclear region. RNase treatment of the cells reduced the Upf2 immunostained signal. The immune-purified fractions containing nuclear and cytoplasmic Upf2 also contained one of the EJC core factors, RBM8A. These results implied the existence of Upf2 in the nucleoplasm and the cytoplasm, and it appeared to be involved in the construction of the mRNA complex. In order to verify the construction of Upf2-binding EJC in the nucleoplasm, an in situ proximity ligation assay was performed with anti-Upf2 and anti-RBM8A antibodies. These results demonstrated that their interaction occurred not only in the cytoplasmic region, but also in the intranuclear region. Taken together, these results suggested that Upf2 combines with EJC in both the cytoplasmic and the intranuclear fractions, and that it is involved in mRNA metabolism in human cells.
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Affiliation(s)
- Takanori Tatsuno
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Yuka Nakamura
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Shaofu Ma
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Naohisa Tomosugi
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920‑0293, Japan
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54
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Brogna S, McLeod T, Petric M. The Meaning of NMD: Translate or Perish. Trends Genet 2016; 32:395-407. [PMID: 27185236 DOI: 10.1016/j.tig.2016.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/02/2016] [Accepted: 04/25/2016] [Indexed: 02/08/2023]
Abstract
Premature translation termination leads to a reduced mRNA level in all types of organisms. In eukaryotes, the phenomenon is known as nonsense-mediated mRNA decay (NMD). This is commonly regarded as the output of a specific surveillance and destruction mechanism that is activated by the presence of a premature translation termination codon (PTC) in an atypical sequence context. Despite two decades of research, it is still unclear how NMD discriminates between PTCs and normal stop codons. We suggest that cells do not possess any such mechanism and instead propose a new model in which this mRNA depletion is a consequence of the appearance of long tracts of mRNA that are unprotected by scanning ribosomes.
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Affiliation(s)
- Saverio Brogna
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK.
| | - Tina McLeod
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
| | - Marija Petric
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT, UK
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55
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McMahon JJ, Miller EE, Silver DL. The exon junction complex in neural development and neurodevelopmental disease. Int J Dev Neurosci 2016; 55:117-123. [PMID: 27071691 DOI: 10.1016/j.ijdevneu.2016.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/28/2016] [Indexed: 11/17/2022] Open
Abstract
Post-transcriptional mRNA metabolism has emerged as a critical regulatory nexus in proper development and function of the nervous system. In particular, recent studies highlight roles for the exon junction complex (EJC) in neurodevelopment. The EJC is an RNA binding complex composed of 3 core proteins, EIF4A3 (DDX48), RBM8A (Y14), and MAGOH, and is a major hub of post-transcriptional regulation. Following deposition onto mRNA, the EJC serves as a platform for the binding of peripheral factors which together regulate splicing, nonsense mediated decay, translation, and RNA localization. While fundamental molecular roles of the EJC have been well established, the in vivo relevance in mammals has only recently been examined. New genetic models and cellular assays have revealed core and peripheral EJC components play critical roles in brain development, stem cell function, neuronal outgrowth, and neuronal activity. Moreover, human genetics studies increasingly implicate EJC components in the etiology of neurodevelopmental disorders. Collectively, these findings indicate that proper dosage of EJC components is necessary for diverse aspects of neuronal development and function. Going forward, genetic models of EJC components will provide valuable tools for further elucidating functions in the nervous system relevant for neurodevelopmental disease.
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Affiliation(s)
- J J McMahon
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, United States
| | - E E Miller
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, United States
| | - D L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, United States; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States; Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710, United States.
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56
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Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE. Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay. Mol Cell Proteomics 2016; 15:1584-97. [PMID: 26896796 DOI: 10.1074/mcp.m115.054056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/31/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) has originally been described as a surveillance mechanism to inhibit the expression of mRNAs with truncated open reading frames (ORFs) and to contribute to the fidelity of gene expression. It is now recognized that NMD also controls the expression of physiological genes with "intact" mRNA. Stress can decrease NMD efficiency and thus increase the mRNA levels of physiological NMD targets. As stress can also inhibit translation, the net outcome for shaping the proteome is difficult to predict. We have thus analyzed de novo protein synthesis in response to NMD inhibition or the induction of mild endoplasmic reticulum (ER) stress by treatment of cells with the reducing agent dithiotreitol (DTT). For this purpose, we combined pulsed azidohomoalanine (AHA) and stable isotope labeling by amino acids in cell culture (SILAC). Labeled proteins were purified by click chemistry-based covalent coupling to agarose beads, trypsinized, fractionated, and analyzed by mass spectrometry (MS). We find that mild ER stress up-regulates the de novo synthesis of components of all three branches of the unfolded protein response (PERK, IRE1 and ATF6) without increasing eIF2α phosphorylation or impairing of protein translation. In contrast, inhibition of NMD induces de novo protein synthesis of downstream targets of the PERK and IRE1 pathways, whereas we could not detect regulation of ATF6-responsive genes. These data thus support a model that implicates a positive feedback loop of ER stress inhibiting NMD efficiency which further promotes the ER stress response in a branch-specific manner.
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Affiliation(s)
- Jana Sieber
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Christian Hauer
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany; ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | - Madhuri Bhuvanagiri
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Stefan Leicht
- ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Gabriele Neu-Yilik
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; ¶European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas E Kulozik
- From the ‡Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany; §Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany;
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57
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Abstract
Nonsense-mediated mRNA decay (NMD) is an mRNA quality-control mechanism that typifies all eukaryotes examined to date. NMD surveys newly synthesized mRNAs and degrades those that harbor a premature termination codon (PTC), thereby preventing the production of truncated proteins that could result in disease in humans. This is evident from dominantly inherited diseases that are due to PTC-containing mRNAs that escape NMD. Although many cellular NMD targets derive from mistakes made during, for example, pre-mRNA splicing and, possibly, transcription initiation, NMD also targets ∼10% of normal physiological mRNAs so as to promote an appropriate cellular response to changing environmental milieus, including those that induce apoptosis, maturation or differentiation. Over the past ∼35 years, a central goal in the NMD field has been to understand how cells discriminate mRNAs that are targeted by NMD from those that are not. In this Cell Science at a Glance and the accompanying poster, we review progress made towards this goal, focusing on human studies and the role of the key NMD factor up-frameshift protein 1 (UPF1).
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
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58
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Hug N, Longman D, Cáceres JF. Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res 2016; 44:1483-95. [PMID: 26773057 PMCID: PMC4770240 DOI: 10.1093/nar/gkw010] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022] Open
Abstract
The Nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. The central role of NMD in the control of gene expression requires the existence of buffering mechanisms that tightly regulate the magnitude of this pathway. Here, we will focus on the mechanism of NMD with an emphasis on the role of RNA helicases in the transition from NMD complexes that recognize a PTC to those that promote mRNA decay. We will also review recent strategies aimed at uncovering novel trans-acting factors and their functional role in the NMD pathway. Finally, we will describe recent progress in the study of the physiological role of the NMD response.
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Affiliation(s)
- Nele Hug
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dasa Longman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Javier F Cáceres
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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59
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Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:61-88. [PMID: 27256382 DOI: 10.1007/978-3-319-29073-7_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, and cellular localization. Most RBPs have distinct mRNA-binding and functional domains; thus, the function of an RBP can be studied independently of RNA-binding by artificially recruiting the RBP to a reporter RNA and then measuring the effect of RBP recruitment on reporter splicing, stability, translational efficiency, or intracellular trafficking. These tethered function assays therefore do not require prior knowledge of the RBP's endogenous RNA targets or its binding sites within these RNAs. Here, we provide an overview of the experimental strategy and the strengths and limitations of common tethering systems. We illustrate specific examples of the application of the assay in elucidating the function of various classes of RBPs. We also discuss how classic tethering assay approaches and insights gained from them have been empowered by more recent technological advances, including efficient genome editing and high-throughput RNA-sequencing.
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60
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Hir HL, Saulière J, Wang Z. The exon junction complex as a node of post-transcriptional networks. Nat Rev Mol Cell Biol 2015; 17:41-54. [DOI: 10.1038/nrm.2015.7] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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61
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Fatscher T, Boehm V, Gehring NH. Mechanism, factors, and physiological role of nonsense-mediated mRNA decay. Cell Mol Life Sci 2015; 72:4523-44. [PMID: 26283621 PMCID: PMC11113733 DOI: 10.1007/s00018-015-2017-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/10/2015] [Accepted: 08/06/2015] [Indexed: 02/04/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent, multistep process that degrades irregular or faulty messenger RNAs (mRNAs). NMD mainly targets mRNAs with a truncated open reading frame (ORF) due to premature termination codons (PTCs). In addition, NMD also regulates the expression of different types of endogenous mRNA substrates. A multitude of factors are involved in the tight regulation of the NMD mechanism. In this review, we focus on the molecular mechanism of mammalian NMD. Based on the published data, we discuss the involvement of translation termination in NMD initiation. Furthermore, we provide a detailed overview of the core NMD machinery, as well as several peripheral NMD factors, and discuss their function. Finally, we present an overview of diseases associated with NMD factor mutations and summarize the current state of treatment for genetic disorders caused by nonsense mutations.
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Affiliation(s)
- Tobias Fatscher
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne, Germany.
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62
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The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Rep 2015; 13:1206-1220. [DOI: 10.1016/j.celrep.2015.09.068] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/31/2015] [Accepted: 09/24/2015] [Indexed: 12/26/2022] Open
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63
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Ajamian L, Abel K, Rao S, Vyboh K, García-de-Gracia F, Soto-Rifo R, Kulozik AE, Gehring NH, Mouland AJ. HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA. Biomolecules 2015; 5:2808-39. [PMID: 26492277 PMCID: PMC4693258 DOI: 10.3390/biom5042808] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022] Open
Abstract
Unspliced, genomic HIV-1 RNA (vRNA) is a component of several ribonucleoprotein complexes (RNP) during the viral replication cycle. In earlier work, we demonstrated that the host upframeshift protein 1 (UPF1), a key factor in nonsense-mediated mRNA decay (NMD), colocalized and associated to the viral structural protein Gag during viral egress. In this work, we demonstrate a new function for UPF1 in the regulation of vRNA nuclear export. OPEN ACCESS Biomolecules 2015, 5 2809 We establish that the nucleocytoplasmic shuttling of UPF1 is required for this function and demonstrate that UPF1 exists in two essential viral RNPs during the late phase of HIV-1 replication: the first, in a nuclear export RNP that contains Rev, CRM1, DDX3 and the nucleoporin p62, and the second, which excludes these nuclear export markers but contains Gag in the cytoplasm. Interestingly, we observed that both UPF2 and the long isoform of UPF3a, UPF3aL, but not the shorter isoforms UPF3aS and UPF3b, are excluded from the UPF1-Rev-CRM1-DDX3 complex as they are negative regulators of vRNA nuclear export. In silico protein-protein docking analyses suggest that Rev binds UPF1 in a region that overlaps the UPF2 binding site, thus explaining the exclusion of this negative regulatory factor by HIV-1 that is necessary for vRNA trafficking. This work uncovers a novel and unique regulatory circuit involving several UPF proteins that ultimately regulate vRNA nuclear export and trafficking.
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Affiliation(s)
- Lara Ajamian
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal QC H3A 2B4, Canada.
| | - Karen Abel
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Kishanda Vyboh
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Biomedical Sciences Institute, Faculty of Medicine, Universidad de Chile, Independencia 8389100, Santiago, Chile.
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Biomedical Sciences Institute, Faculty of Medicine, Universidad de Chile, Independencia 8389100, Santiago, Chile.
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg 69120, Germany.
- European Molecular Biology Laboratory, Partnership Unit, University of Heidelberg Molecular Medicine, Heidelberg 69117, Germany.
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne 50674, Germany.
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal QC H3A 2B4, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
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64
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He F, Jacobson A. Nonsense-Mediated mRNA Decay: Degradation of Defective Transcripts Is Only Part of the Story. Annu Rev Genet 2015; 49:339-66. [PMID: 26436458 DOI: 10.1146/annurev-genet-112414-054639] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance mechanism that monitors cytoplasmic mRNA translation and targets mRNAs undergoing premature translation termination for rapid degradation. From yeasts to humans, activation of NMD requires the function of the three conserved Upf factors: Upf1, Upf2, and Upf3. Here, we summarize the progress in our understanding of the molecular mechanisms of NMD in several model systems and discuss recent experiments that address the roles of Upf1, the principal regulator of NMD, in the initial targeting and final degradation of NMD-susceptible mRNAs. We propose a unified model for NMD in which the Upf factors provide several functions during premature termination, including the stimulation of release factor activity and the dissociation and recycling of ribosomal subunits. In this model, the ultimate degradation of the mRNA is the last step in a complex premature termination process.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655; ,
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655; ,
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65
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Lykke-Andersen S, Jensen TH. Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes. Nat Rev Mol Cell Biol 2015; 16:665-77. [PMID: 26397022 DOI: 10.1038/nrm4063] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is probably the best characterized eukaryotic RNA degradation pathway. Through intricate steps, a set of NMD factors recognize and degrade mRNAs with translation termination codons that are positioned in abnormal contexts. However, NMD is not only part of a general cellular quality control system that prevents the production of aberrant proteins. Mammalian cells also depend on NMD to dynamically adjust their transcriptomes and their proteomes to varying physiological conditions. In this Review, we discuss how NMD targets mRNAs, the types of mRNAs that are targeted, and the roles of NMD in cellular stress, differentiation and maturation processes.
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Affiliation(s)
- Søren Lykke-Andersen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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66
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Zou D, McSweeney C, Sebastian A, Reynolds DJ, Dong F, Zhou Y, Deng D, Wang Y, Liu L, Zhu J, Zou J, Shi Y, Albert I, Mao Y. A critical role of RBM8a in proliferation and differentiation of embryonic neural progenitors. Neural Dev 2015; 10:18. [PMID: 26094033 PMCID: PMC4479087 DOI: 10.1186/s13064-015-0045-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/17/2015] [Indexed: 02/04/2023] Open
Abstract
Background Nonsense mediated mRNA decay (NMD) is an RNA surveillance mechanism that controls RNA stability and ensures the speedy degradation of erroneous and unnecessary transcripts. This mechanism depends on several core factors in the exon junction complex (EJC), eIF4A3, RBM8a, Magoh, and BTZ, as well as peripheral factors to distinguish premature stop codons (PTCs) from normal stop codons in transcripts. Recently, emerging evidence has indicated that NMD factors are associated with neurodevelopmental disorders such as autism spectrum disorder (ASD) and intellectual disability (ID). However, the mechanism in which these factors control embryonic brain development is not clear. Result We found that RBM8a is critical for proliferation and differentiation in cortical neural progenitor cells (NPCs). RBM8a is highly expressed in the subventricular zone (SVZ) of the early embryonic cortex, suggesting that RBM8a may play a role in regulating NPCs. RBM8a overexpression stimulates embryonic NPC proliferation and suppresses neuronal differentiation. Conversely, knockdown of RBM8a in the neocortex reduces NPC proliferation and promotes premature neuronal differentiation. Moreover, overexpression of RBM8a suppresses cell cycle exit and keeps cortical NPCs in a proliferative state. To uncover the underlying mechanisms of this phenotype, genome-wide RNAseq was used to identify potential downstream genes of RBM8a in the brain, which have been implicated in autism and neurodevelopmental disorders. Interestingly, autism and schizophrenia risk genes are highly represented in downstream transcripts of RBM8a. In addition, RBM8a regulates multiple alternative splicing genes and NMD targets that are implicated in ASD. Taken together, this data suggests a novel role of RBM8a in the regulation of neurodevelopment. Conclusions Our studies provide some insight into causes of mental illnesses and will facilitate the development of new therapeutic strategies for neurodevelopmental illnesses. Electronic supplementary material The online version of this article (doi:10.1186/s13064-015-0045-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donghua Zou
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China. .,Department of Geriatrics, The 303 Hospital of Chinese People's Liberation Army, Nanning, Guangxi Province, 530021, China. .,Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Colleen McSweeney
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Aswathy Sebastian
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Derrick James Reynolds
- Department of Microbiology & Molecular Genetics School of Medicine, University of California, Irvine, CA, 92697, USA.
| | - Fengping Dong
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Yijing Zhou
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Dazhi Deng
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Emergency, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, Guangxi Province, 530021, China.
| | - Yonggang Wang
- Department of Neurology, School of Medicine, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200127, China.
| | - Long Liu
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, 410073, China.
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA.
| | - Jizhong Zou
- Center for Molecular Medicine, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA.
| | - Yongsheng Shi
- Department of Microbiology & Molecular Genetics School of Medicine, University of California, Irvine, CA, 92697, USA.
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Yingwei Mao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Province, 530021, China. .,Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
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Alrahbeni T, Sartor F, Anderson J, Miedzybrodzka Z, McCaig C, Müller B. Full UPF3B function is critical for neuronal differentiation of neural stem cells. Mol Brain 2015; 8:33. [PMID: 26012578 PMCID: PMC4445987 DOI: 10.1186/s13041-015-0122-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/11/2015] [Indexed: 12/03/2022] Open
Abstract
Background Mutation in the UPF3B gene on chromosome X is implicated in neurodevelopmental disorders including X-linked intellectual disability, autism and schizophrenia. The protein UPF3B is involved in the nonsense-mediated mRNA decay pathway (NMD) that controls mRNA stability and functions in the prevention of the synthesis of truncated proteins. Results Here we show that NMD pathway components UPF3B and UPF1 are down-regulated during differentiation of neural stem cells into neurons. Using tethered function assays we found that UPF3B missense mutations described in families with neurodevelopmental disorders reduced the activity of UPF3B protein in NMD. In neural stem cells, UPF3B protein was detected in the cytoplasm and in the nucleus. Similarly in neurons, UPF3B protein was detected in neurites, the somatic cytoplasm and in the nucleus. In both cell types nuclear UPF3B protein was enriched in the nucleolus. Using GFP tagged UPF3B proteins we found that the missense mutations did not affect the cellular localisation. Expression of missense mutant UPF3B disturbed neuronal differentiation and reduced the complexity of the branching of neurites. Neuronal differentiation was similarly affected in the presence of the NMD inhibitor Amlexanox. The expression of mutant UPF3B proteins lead to a subtle increase in mRNA levels of selected NMD targets. Conclusions Together our findings indicate that, despite the down-regulation of NMD factors, functional NMD is critical for neuronal differentiation. We propose that the neurodevelopmental phenotype of UPF3B missense mutation is caused by impairment of NMD function altering neuronal differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s13041-015-0122-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tahani Alrahbeni
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK. .,Current address: Riyadh Colleges of Dentistry and Pharmacy, Olaya Campus, Riyadh, Saudi Arabia.
| | - Francesca Sartor
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
| | - Jihan Anderson
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
| | - Zosia Miedzybrodzka
- Medical Genetics, Polwarth Building, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
| | - Colin McCaig
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
| | - Berndt Müller
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
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68
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Shi M, Zhang H, Wang L, Zhu C, Sheng K, Du Y, Wang K, Dias A, Chen S, Whitman M, Wang E, Reed R, Cheng H. Premature Termination Codons Are Recognized in the Nucleus in A Reading-Frame Dependent Manner. Cell Discov 2015; 1. [PMID: 26491543 PMCID: PMC4610414 DOI: 10.1038/celldisc.2015.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
mRNAs containing premature termination codons (PTCs) are known to be degraded via nonsense-mediated mRNA decay (NMD). Unexpectedly, we found that mRNAs containing any type of PTC (UAA, UAG, UGA) are detained in the nucleus whereas their wild-type counterparts are rapidly exported. This retention is strictly reading-frame dependent. Strikingly, our data indicate that translating ribosomes in the nucleus proofread the frame and detect the PTCs in the nucleus. Moreover, the shuttling NMD protein Upf1 specifically associates with PTC+ mRNA in the nucleus and is required for nuclear retention of PTC+ mRNA. Together, our data lead to a working model that PTCs are recognized in the nucleus by translating ribosomes, resulting in recruitment of Upf1, which in turn functions in nuclear retention of PTC+ mRNA. Nuclear PTC recognition adds a new layer of proofreading for mRNA and may be vital for ensuring the extraordinary fidelity required for protein production.
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Affiliation(s)
- Min Shi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Heng Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lantian Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changlan Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Sheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhua Du
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Anusha Dias
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Enduo Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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69
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Toma KG, Rebbapragada I, Durand S, Lykke-Andersen J. Identification of elements in human long 3' UTRs that inhibit nonsense-mediated decay. RNA (NEW YORK, N.Y.) 2015; 21:887-97. [PMID: 25805855 PMCID: PMC4408796 DOI: 10.1261/rna.048637.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway serves an important role in gene expression by targeting aberrant mRNAs that have acquired premature termination codons (PTCs) as well as a subset of normally processed endogenous mRNAs. One determinant for the targeting of mRNAs by NMD is the occurrence of translation termination distal to the poly(A) tail. Yet, a large subset of naturally occurring mRNAs contain long 3' UTRs, many of which, according to global studies, are insensitive to NMD. This raises the possibility that such mRNAs have evolved mechanisms for NMD evasion. Here, we analyzed a set of human long 3' UTR mRNAs and found that many are indeed resistant to NMD. By dissecting the 3' UTR of one such mRNA, TRAM1 mRNA, we identified a cis element located within the first 200 nt that inhibits NMD when positioned in downstream proximity of the translation termination codon and is sufficient for repressing NMD of a heterologous reporter mRNA. Investigation of other NMD-evading long 3' UTR mRNAs revealed a subset that, similar to TRAM1 mRNA, contains NMD-inhibiting cis elements in the first 200 nt. A smaller subset of long 3' UTR mRNAs evades NMD by a different mechanism that appears to be independent of a termination-proximal cis element. Our study suggests that different mechanisms have evolved to ensure NMD evasion of human mRNAs with long 3' UTRs.
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Affiliation(s)
- Kalodiah G Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Indrani Rebbapragada
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Sébastien Durand
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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70
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Chuang TW, Lee KM, Tarn WY. Function and pathological implications of exon junction complex factor Y14. Biomolecules 2015; 5:343-55. [PMID: 25866920 PMCID: PMC4496676 DOI: 10.3390/biom5020343] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic mRNA biogenesis involves a series of interconnected steps, including nuclear pre-mRNA processing, mRNA export, and surveillance. The exon-junction complex (EJC) is deposited on newly spliced mRNAs and coordinates several downstream steps of mRNA biogenesis. The EJC core protein, Y14, functions with its partners in nonsense-mediated mRNA decay and translational enhancement. Y14 plays additional roles in mRNA metabolism, some of which are independent of the EJC, and it is also involved in other cellular processes. Genetic mutations or aberrant expression of Y14 results in physiological abnormality and may cause disease. Therefore, it is important to understand the various functions of Y14 and its physiological and pathological roles.
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Affiliation(s)
- Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Kou-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
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71
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Wolniak SM, Boothby TC, van der Weele CM. Posttranscriptional control over rapid development and ciliogenesis in Marsilea. Methods Cell Biol 2015; 127:403-44. [PMID: 25837402 DOI: 10.1016/bs.mcb.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Marsilea vestita is a semiaquatic fern that produces its spores (meiotic products) as it undergoes a process of natural desiccation. During the period of desiccation, the spores mature, and produce large quantities of pre-mRNA, which is partially processed and stored in nuclear speckles and can remain stable during a period of extended quiescence in the dry spore. Rehydration of the spores initiates a highly coordinated developmental program, featuring nine successive mitotic division cycles that occur at precise times and in precise planes within the spore wall to produce 39 cells, 32 of which are spermatids. The spermatids then undergo de novo basal body formation, the assembly of a massive cytoskeleton, nuclear and cell elongation, and finally ciliogenesis, before being released from the spore wall. The entire developmental program requires only 11 h to reach completion, and is synchronous in a population of spores rehydrated at the same time. Rapid development in this endosporic gametophyte is controlled posttranscriptionally, where stored pre-mRNAs, many of which are intron-retaining transcripts, are unmasked, processed, and translated under tight spatial and temporal control. Here, we describe posttranscriptional mechanisms that exert temporal and spatial control over this developmental program, which culminates in the production of ∼140 ciliary axonemes in each spermatozoid.
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Affiliation(s)
- Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Thomas C Boothby
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Corine M van der Weele
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
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72
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Boehm V, Haberman N, Ottens F, Ule J, Gehring NH. 3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons. Cell Rep 2014; 9:555-68. [PMID: 25310981 DOI: 10.1016/j.celrep.2014.09.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/05/2014] [Accepted: 09/07/2014] [Indexed: 11/16/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) degrades different classes of mRNAs, including transcripts with premature termination codons (PTCs). The NMD factor SMG6 initiates degradation of substrate mRNAs by endonucleolytic cleavage. Here, we aim to delineate the cascade of NMD-activating events that culminate in endocleavage. We report that long 3' UTRs elicit SMG6-mediated endonucleolytic degradation. The presence of an exon-junction complex (EJC) within the 3' UTR strongly stimulates endocleavage in a distance-independent manner. The interaction of SMG6 with EJCs is not required for endocleavage. Whereas the core NMD component UPF2 supports endonucleolytic decay of long 3' UTR mRNAs, it is mostly dispensable during EJC-stimulated endocleavage. Using high-throughput sequencing, we map endocleavage positions of different PTC-containing reporter mRNAs and an endogenous NMD substrate to regions directly at and downstream of the termination codon. These results reveal how messenger ribonucleoprotein (mRNP) parameters differentially influence SMG6-executed endonucleolysis and uncover central characteristics of this phenomenon associated with translation termination.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Franziska Ottens
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
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73
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Abstract
The exon junction complex (EJC) plays a central role in controlling RNA fate and aids faithful splicing of pre-mRNAs containing large introns via an unknown mechanism. Brennecke and colleagues show that the core EJC plus the accessory factors RnpS1 and Acinus aid in the definition and efficient splicing of neighboring introns. Interestingly, the most highly affected intron belongs to the piwi locus, which explains the reported transposon desilencing in EJC-depleted Drosophila ovaries. Based on transcriptome-wide analysis, the authors propose that the dependency of splicing on the EJC is exploited to control the temporal order of splicing events. Splicing of pre-mRNAs results in the deposition of the exon junction complex (EJC) upstream of exon–exon boundaries. The EJC plays crucial post-splicing roles in export, translation, localization, and nonsense-mediated decay of mRNAs. It also aids faithful splicing of pre-mRNAs containing large introns, albeit via an unknown mechanism. Here, we show that the core EJC plus the accessory factors RnpS1 and Acinus aid in definition and efficient splicing of neighboring introns. This requires prior deposition of the EJC in close proximity to either an upstream or downstream splicing event. If present in isolation, EJC-dependent introns are splicing-defective also in wild-type cells. Interestingly, the most affected intron belongs to the piwi locus, which explains the reported transposon desilencing in EJC-depleted Drosophila ovaries. Based on a transcriptome-wide analysis, we propose that the dependency of splicing on the EJC is exploited as a means to control the temporal order of splicing events.
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74
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Chakrabarti S, Bonneau F, Schüssler S, Eppinger E, Conti E. Phospho-dependent and phospho-independent interactions of the helicase UPF1 with the NMD factors SMG5-SMG7 and SMG6. Nucleic Acids Res 2014; 42:9447-60. [PMID: 25013172 PMCID: PMC4132714 DOI: 10.1093/nar/gku578] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that recognizes mRNAs with premature stop codons and targets them for rapid degradation. Evidence from previous studies has converged on UPF1 as the central NMD factor. In human cells, the SMG1 kinase phosphorylates UPF1 at the N-terminal and C-terminal tails, in turn allowing the recruitment of the NMD factors SMG5, SMG6 and SMG7. To understand the molecular mechanisms, we recapitulated these steps of NMD in vitro using purified components. We find that a short C-terminal segment of phosphorylated UPF1 containing the last two Ser-Gln motifs is recognized by the heterodimer of SMG5 and SMG7 14–3–3-like proteins. In contrast, the SMG6 14–3–3-like domain is a monomer. The crystal structure indicates that the phosphoserine binding site of the SMG6 14–3–3-like domain is similar to that of SMG5 and can mediate a weak phospho-dependent interaction with UPF1. The dominant SMG6–UPF1 interaction is mediated by a low-complexity region bordering the 14–3–3-like domain of SMG6 and by the helicase domain and C-terminal tail of UPF1. This interaction is phosphorylation independent. Our study demonstrates that SMG5–SMG7 and SMG6 exhibit different and non-overlapping modes of UPF1 recognition, thus pointing at distinguished roles in integrating the complex NMD interaction network.
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Affiliation(s)
- Sutapa Chakrabarti
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Fabien Bonneau
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Steffen Schüssler
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Elfriede Eppinger
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Elena Conti
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
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75
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Lykke-Andersen J, Bennett EJ. Protecting the proteome: Eukaryotic cotranslational quality control pathways. ACTA ACUST UNITED AC 2014; 204:467-76. [PMID: 24535822 PMCID: PMC3926952 DOI: 10.1083/jcb.201311103] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, ribosomal, and/or nascent polypeptide components, thereby clearing the cell of improper translation products and defective components of the translation machinery.
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Affiliation(s)
- Jens Lykke-Andersen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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76
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Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 2013; 505:117-20. [PMID: 24284625 PMCID: PMC3877715 DOI: 10.1038/nature12730] [Citation(s) in RCA: 2841] [Impact Index Per Article: 258.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 10/03/2013] [Indexed: 12/20/2022]
Abstract
N(6)-methyladenosine (m(6)A) is the most prevalent internal (non-cap) modification present in the messenger RNA of all higher eukaryotes. Although essential to cell viability and development, the exact role of m(6)A modification remains to be determined. The recent discovery of two m(6)A demethylases in mammalian cells highlighted the importance of m(6)A in basic biological functions and disease. Here we show that m(6)A is selectively recognized by the human YTH domain family 2 (YTHDF2) 'reader' protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m(6)A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies. The carboxy-terminal domain of YTHDF2 selectively binds to m(6)A-containing mRNA, whereas the amino-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. Our results indicate that the dynamic m(6)A modification is recognized by selectively binding proteins to affect the translation status and lifetime of mRNA.
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Affiliation(s)
- Xiao Wang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Adrian Gomez
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Gary C Hon
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, UCSD Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Yanan Yue
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Dali Han
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Ye Fu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Marc Parisien
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Guifang Jia
- 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA [2] Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, UCSD Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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Clerici M, Deniaud A, Boehm V, Gehring NH, Schaffitzel C, Cusack S. Structural and functional analysis of the three MIF4G domains of nonsense-mediated decay factor UPF2. Nucleic Acids Res 2013; 42:2673-86. [PMID: 24271394 PMCID: PMC3936715 DOI: 10.1093/nar/gkt1197] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated decay (NMD) is a eukaryotic quality control pathway, involving conserved proteins UPF1, UPF2 and UPF3b, which detects and degrades mRNAs with premature stop codons. Human UPF2 comprises three tandem MIF4G domains and a C-terminal UPF1 binding region. MIF4G-3 binds UPF3b, but the specific functions of MIF4G-1 and MIF4G-2 are unknown. Crystal structures show that both MIF4G-1 and MIF4G-2 contain N-terminal capping helices essential for stabilization of the 10-helix MIF4G core and that MIF4G-2 interacts with MIF4G-3, forming a rigid assembly. The UPF2/UPF3b/SMG1 complex is thought to activate the kinase SMG1 to phosphorylate UPF1 in vivo. We identify MIF4G-3 as the binding site and in vitro substrate of SMG1 kinase and show that a ternary UPF2 MIF4G-3/UPF3b/SMG1 complex can form in vitro. Whereas in vivo complementation assays show that MIF4G-1 and MIF4G-2 are essential for NMD, tethering assays reveal that UPF2 truncated to only MIF4G-3 and the UPF1-binding region can still partially accomplish NMD. Thus UPF2 MIF4G-1 and MIF4G-2 appear to have a crucial scaffolding role, while MIF4G-3 is the key module required for triggering NMD.
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Affiliation(s)
- Marcello Clerici
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France, Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France and University of Cologne, Institute for Genetics, Zuelpicher Street 47a, 50674 Cologne, Germany
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78
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Nonsense-mediated mRNA decay: inter-individual variability and human disease. Neurosci Biobehav Rev 2013; 46 Pt 2:175-86. [PMID: 24239855 DOI: 10.1016/j.neubiorev.2013.10.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 01/09/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a regulatory pathway that functions to degrade transcripts containing premature termination codons (PTCs) and to maintain normal transcriptome homeostasis. Nonsense and frameshift mutations that generate PTCs cause approximately one-third of all known human genetic diseases and thus NMD has a potentially important role in human disease. In genetic disorders in which the affected genes carry PTC-generating mutations, NMD acts as a double-edge sword. While it can benefit the patient by degrading PTC-containing mRNAs that encode detrimental, dominant-negative truncated proteins, it can also make the disease worse when a PTC-containing mRNA is degraded that encodes a mutant but still functional protein. There is evidence that the magnitude of NMD varies between individuals, which, in turn, has been shown to correlate with both clinical presentations and the patients' responses to drugs that promote read-through of PTCs. In this review, we examine the evidence supporting the existence of inter-individual variability in NMD efficiency and discuss the genetic factors that underlie this variability. We propose that inter-individual variability in NMD efficiency is a common phenomenon in human populations and that an individual's NMD efficiency should be taken into consideration when testing, developing, and making therapeutic decisions for diseases caused by genes harboring PTCs.
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79
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Metze S, Herzog VA, Ruepp MD, Mühlemann O. Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways. RNA (NEW YORK, N.Y.) 2013; 19:1432-48. [PMID: 23962664 PMCID: PMC3854533 DOI: 10.1261/rna.038893.113] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 07/08/2013] [Indexed: 05/18/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic post-transcriptional gene regulation mechanism that eliminates mRNAs with the termination codon (TC) located in an unfavorable environment for efficient translation termination. The best-studied NMD-targeted mRNAs contain premature termination codons (PTCs); however, NMD regulates even many physiological mRNAs. An exon-junction complex (EJC) located downstream from a TC acts as an NMD-enhancing signal, but is not generally required for NMD. Here, we compared these "EJC-enhanced" and "EJC-independent" modes of NMD with regard to their requirement for seven known NMD factors in human cells using two well-characterized NMD reporter genes (immunoglobulin μ and β-Globin) with or without an intron downstream from the PTC. We show that both NMD modes depend on UPF1 and SMG1, but detected transcript-specific differences with respect to the requirement for UPF2 and UPF3b, consistent with previously reported UPF2- and UPF3-independent branches of NMD. In addition and contrary to expectation, a higher sensitivity of EJC-independent NMD to reduced UPF2 and UPF3b concentrations was observed. Our data further revealed a redundancy of the endo- and exonucleolytic mRNA degradation pathways in both modes of NMD. Moreover, the relative contributions of both decay pathways differed between the reporters, with PTC-containing immunoglobulin μ transcripts being preferentially subjected to SMG6-mediated endonucleolytic cleavage, whereas β-Globin transcripts were predominantly degraded by the SMG5/SMG7-dependent pathway. Overall, the surprising heterogeneity observed with only two NMD reporter pairs suggests the existence of several mechanistically distinct branches of NMD in human cells.
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Affiliation(s)
- Stefanie Metze
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Veronika A. Herzog
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
- Corresponding authorE-mail
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80
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Martin RM, Rino J, Carvalho C, Kirchhausen T, Carmo-Fonseca M. Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep 2013; 4:1144-55. [PMID: 24035393 DOI: 10.1016/j.celrep.2013.08.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 05/20/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022] Open
Abstract
Removal of introns from pre-messenger RNAs (pre-mRNAs) via splicing provides a versatile means of genetic regulation that is often disrupted in human diseases. To decipher how splicing occurs in real time, we directly examined with single-molecule sensitivity the kinetics of intron excision from pre-mRNA in the nucleus of living human cells. By using two different RNA labeling methods, MS2 and λN, we show that β-globin introns are transcribed and excised in 20-30 s. Furthermore, we show that replacing the weak polypyrimidine (Py) tract in mouse immunoglobulin μ (IgM) pre-mRNA by a U-rich Py decreases the intron lifetime, thus providing direct evidence that splice-site strength influences splicing kinetics. We also found that RNA polymerase II transcribes at elongation rates ranging between 3 and 6 kb min(-1) and that transcription can be rate limiting for splicing. These results have important implications for a mechanistic understanding of cotranscriptional splicing regulation in the live-cell context.
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Affiliation(s)
- Robert M Martin
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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81
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Leoyklang P, Suphapeetiporn K, Srichomthong C, Tongkobpetch S, Fietze S, Dorward H, Cullinane AR, Gahl WA, Huizing M, Shotelersuk V. Disorders with similar clinical phenotypes reveal underlying genetic interaction: SATB2 acts as an activator of the UPF3B gene. Hum Genet 2013; 132:1383-93. [PMID: 23925499 DOI: 10.1007/s00439-013-1345-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/24/2013] [Indexed: 01/01/2023]
Abstract
Two syndromic cognitive impairment disorders have very similar craniofacial dysmorphisms. One is caused by mutations of SATB2, a transcription regulator and the other by heterozygous mutations leading to premature stop codons in UPF3B, encoding a member of the nonsense-mediated mRNA decay complex. Here we demonstrate that the products of these two causative genes function in the same pathway. We show that the SATB2 nonsense mutation in our patient leads to a truncated protein that localizes to the nucleus, forms a dimer with wild-type SATB2 and interferes with its normal activity. This suggests that the SATB2 nonsense mutation has a dominant negative effect. The patient's leukocytes had significantly decreased UPF3B mRNA compared to controls. This effect was replicated both in vitro, where siRNA knockdown of SATB2 in HEK293 cells resulted in decreased UPF3B expression, and in vivo, where embryonic tissue of Satb2 knockout mice showed significantly decreased Upf3b expression. Furthermore, chromatin immunoprecipitation demonstrates that SATB2 binds to the UPF3B promoter, and a luciferase reporter assay confirmed that SATB2 expression significantly activates gene transcription using the UPF3B promoter. These findings indicate that SATB2 activates UPF3B expression through binding to its promoter. This study emphasizes the value of recognizing disorders with similar clinical phenotypes to explore underlying mechanisms of genetic interaction.
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Affiliation(s)
- Petcharat Leoyklang
- Biomedical Science Program, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
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82
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Serquiña AKP, Das SR, Popova E, Ojelabi OA, Roy CK, Göttlinger HG. UPF1 is crucial for the infectivity of human immunodeficiency virus type 1 progeny virions. J Virol 2013; 87:8853-61. [PMID: 23785196 PMCID: PMC3754033 DOI: 10.1128/jvi.00925-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 06/10/2013] [Indexed: 12/28/2022] Open
Abstract
The SF1 helicase MOV10 is an antiviral factor that is incorporated into human immunodeficiency virus type 1 (HIV-1) virions. We now report that HIV-1 virions also incorporate UPF1, which belongs to the same SF1 helicase subfamily as MOV10 and functions in the nonsense-mediated decay (NMD) pathway. Unlike ectopic MOV10, the overexpression of UPF1 does not impair the infectivity of HIV-1 progeny virions. However, UPF1 becomes a potent inhibitor of HIV-1 progeny virion infectivity when residues required for its helicase activity are mutated. In contrast, equivalent mutations abolish the antiviral activity of MOV10. Importantly, cells depleted of endogenous UPF1, but not of another NMD core component, produce HIV-1 virions of substantially lower specific infectivity. The defect is at the level of reverse transcription, the same stage of the HIV-1 life cycle inhibited by ectopic MOV10. Thus, whereas ectopic MOV10 restricts HIV-1 replication, the related UPF1 helicase functions as a cofactor at an early postentry step.
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Affiliation(s)
| | - Suman R. Das
- Program in Gene Function and Expression, Program in Molecular Medicine
| | - Elena Popova
- Program in Gene Function and Expression, Program in Molecular Medicine
| | - Ogooluwa A. Ojelabi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christian K. Roy
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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83
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Singh KK, Wachsmuth L, Kulozik AE, Gehring NH. Two mammalian MAGOH genes contribute to exon junction complex composition and nonsense-mediated decay. RNA Biol 2013; 10:1291-8. [PMID: 23917022 PMCID: PMC3817150 DOI: 10.4161/rna.25827] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The exon junction complex (EJC) participates in the regulation of many post-transcriptional steps of gene expression. EJCs are deposited on messenger RNAs (mRNAs) during splicing and their core consists of eIF4A3, MLN51, Y14, and MAGOH. Here, we show that two genes encoding MAGOH paralogs (referred to as MAGOH and MAGOHB) are expressed in mammals. In macrophages, the expression of MAGOHB, but not MAGOH mRNA, increases rapidly after LPS stimulation. Both MAGOH proteins interact with other EJC components, incorporate into mRNA-bound EJCs, and activate nonsense-mediated decay. Furthermore, the simultaneous depletion of MAGOH and MAGOHB, but not individual depletions, impair nonsense-mediated decay in human cells. Hence, our results establish that the core composition of mammalian EJCs is more complex than previously recognized.
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Affiliation(s)
- Kusum K Singh
- University of Cologne; Institute for Genetics; Cologne, Germany
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84
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Jolly LA, Homan CC, Jacob R, Barry S, Gecz J. The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth. Hum Mol Genet 2013; 22:4673-87. [PMID: 23821644 DOI: 10.1093/hmg/ddt315] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Loss-of-function mutations in UPF3B result in variable clinical presentations including intellectual disability (ID, syndromic and non-syndromic), autism, childhood onset schizophrenia and attention deficit hyperactivity disorder. UPF3B is a core member of the nonsense-mediated mRNA decay (NMD) pathway that functions to rapidly degrade transcripts with premature termination codons (PTCs). Traditionally identified in thousands of human diseases, PTCs were recently also found to be part of 'normal' genetic variation in human populations. Furthermore, many human transcripts have naturally occurring regulatory features compatible with 'endogenous' PTCs strongly suggesting roles of NMD beyond PTC mRNA control. In this study, we investigated the role of Upf3b and NMD in neural cells. We provide evidence that suggests Upf3b-dependent NMD (Upf3b-NMD) is regulated at multiple levels during development including regulation of expression and sub-cellular localization of Upf3b. Furthermore, complementary expression of Upf3b, Upf3a and Stau1 stratify the developing dorsal telencephalon, suggesting that alternative NMD, and the related Staufen1-mediated mRNA decay (SMD) pathways are differentially employed. A loss of Upf3b-NMD in neural progenitor cells (NPCs) resulted in the expansion of cell numbers at the expense of their differentiation. In primary hippocampal neurons, loss of Upf3b-NMD resulted in subtle neurite growth effects. Our data suggest that the cellular consequences of loss of Upf3b-NMD can be explained in-part by changes in expression of key NMD-feature containing transcripts, which are commonly deregulated also in patients with UPF3B mutations. Our research identifies novel pathological mechanisms of UPF3B mutations and at least partly explains the clinical phenotype of UPF3B patients.
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Affiliation(s)
- Lachlan A Jolly
- Department of Genetic and Molecular Pathology, SA Pathology, North Adelaide 5006, Australia
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85
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Giannandrea M, Guarnieri FC, Gehring NH, Monzani E, Benfenati F, Kulozik AE, Valtorta F. Nonsense-mediated mRNA decay and loss-of-function of the protein underlie the X-linked epilepsy associated with the W356× mutation in synapsin I. PLoS One 2013; 8:e67724. [PMID: 23818987 PMCID: PMC3688603 DOI: 10.1371/journal.pone.0067724] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/21/2013] [Indexed: 11/22/2022] Open
Abstract
Synapsins are a family of neuronal phosphoproteins associated with the cytosolic surface of synaptic vesicles. Experimental evidence suggests a role for synapsins in synaptic vesicle clustering and recycling at the presynaptic terminal, as well as in neuronal development and synaptogenesis. Synapsin knock-out (Syn1(-/-) ) mice display an epileptic phenotype and mutations in the SYN1 gene have been identified in individuals affected by epilepsy and/or autism spectrum disorder. We investigated the impact of the c.1067G>A nonsense transition, the first mutation described in a family affected by X-linked syndromic epilepsy, on the expression and functional properties of the synapsin I protein. We found that the presence of a premature termination codon in the human SYN1 transcript renders it susceptible to nonsense-mediated mRNA decay (NMD). Given that the NMD efficiency is highly variable among individuals and cell types, we investigated also the effects of expression of the mutant protein and found that it is expressed at lower levels compared to wild-type synapsin I, forms perinuclear aggregates and is unable to reach presynaptic terminals in mature hippocampal neurons grown in culture. Taken together, these data indicate that in patients carrying the W356× mutation the function of synapsin I is markedly impaired, due to both the strongly decreased translation and the altered function of the NMD-escaped protein, and support the value of Syn1(-/-) mice as an experimental model mimicking the human pathology.
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MESH Headings
- Animals
- Blotting, Northern
- Cells, Cultured
- Codon, Nonsense
- Epilepsy/genetics
- Epilepsy/metabolism
- Female
- Gene Expression
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/metabolism
- HeLa Cells
- Hippocampus/cytology
- Hippocampus/metabolism
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microscopy, Fluorescence
- Microtubule-Associated Proteins/metabolism
- Neurons/metabolism
- Nonsense Mediated mRNA Decay
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Rats, Sprague-Dawley
- Synapsins/genetics
- Synapsins/metabolism
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Affiliation(s)
- Maila Giannandrea
- Division of Neuroscience, San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy
| | - Fabrizia C. Guarnieri
- Division of Neuroscience, San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy
| | | | - Elena Monzani
- Division of Neuroscience, San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy
| | - Fabio Benfenati
- Department of Neuroscience and Brain Technologies, The Italian Institute of Technology, Genoa, Italy
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Andreas E. Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg Medical Center and Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Flavia Valtorta
- Division of Neuroscience, San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy
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86
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Geißler V, Altmeyer S, Stein B, Uhlmann-Schiffler H, Stahl H. The RNA helicase Ddx5/p68 binds to hUpf3 and enhances NMD of Ddx17/p72 and Smg5 mRNA. Nucleic Acids Res 2013; 41:7875-88. [PMID: 23788676 PMCID: PMC3763533 DOI: 10.1093/nar/gkt538] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Non-sense-mediated mRNA decay (NMD) is a mechanism of translation-dependent mRNA surveillance in eukaryotes: it degrades mRNAs with premature termination codons (PTCs) and contributes to cellular homeostasis by downregulating a number of physiologically important mRNAs. In the NMD pathway, Upf proteins, a set of conserved factors of which Upf1 is the central regulator, recruit decay enzymes to promote RNA cleavage. In mammals, the degradation of PTC-containing mRNAs is triggered by the exon–junction complex (EJC) through binding of its constituents Upf2 and Upf3 to Upf1. The complex formed eventually induces translational repression and recruitment of decay enzymes. Mechanisms by which physiological mRNAs are targeted by the NMD machinery in the absence of an EJC have been described but still are discussed controversially. Here, we report that the DEAD box proteins Ddx5/p68 and its paralog Ddx17/p72 also bind the Upf complex by physical interaction with Upf3, thereby interfering with the binding of EJC. By activating the NMD machinery, Ddx5 is shown to regulate the expression of its own, Ddx17 and Smg5 mRNAs. For NMD triggering, the adenosine triphosphate-binding activity of Ddx5 and the 3′-untranslated region of substrate mRNAs are essential.
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Affiliation(s)
- Verena Geißler
- Department of Medical Biochemistry and Molecular Biology, University of Saarland, Medical Center, Building 45, 66421 Homburg, Germany
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87
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Nakano K, Ando T, Yamagishi M, Yokoyama K, Ishida T, Ohsugi T, Tanaka Y, Brighty DW, Watanabe T. Viral interference with host mRNA surveillance, the nonsense-mediated mRNA decay (NMD) pathway, through a new function of HTLV-1 Rex: implications for retroviral replication. Microbes Infect 2013; 15:491-505. [PMID: 23541980 DOI: 10.1016/j.micinf.2013.03.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 01/08/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an essential and conserved cellular mRNA quality control mechanism. RNA signals to express viral genes from overlapping open reading frames potentially initiate NMD, nevertheless it is not clear whether viral RNAs are sensitive to NMD or if viruses have evolved mechanisms to evade NMD. Here we demonstrate that the genomic and full-length mRNAs of Human-T-cell Leukemia Virus type-I (HTLV-1), a retrovirus responsible for Adult T-cell Leukemia (ATL), are sensitive to NMD. They exhibit accelerated turnover in NMD-activated cells, while siRNA-mediated knockdown of NMD-master-regulator, UPF1, promotes enhanced stability of them. These effects on RNA stability were recapitulated by a reporter construct encoding the HTLV-1 translational frameshift signal of gag-pol. In agreement with the RNA stability, viral protein expression from the integrated provirus was inversely correlated with cellular NMD activity. We further demonstrated that the viral RNA-binding protein, Rex, approves the stability of viral RNA by inhibiting NMD. Significantly, Rex establishes a general block to NMD, as both NMD-responsive reporter transcripts and natural host-encoded NMD substrates were stabilized in the presence of Rex. Thus, we suggest that Rex not only stabilizes viral transcripts, but also perturbs cellular mRNA metabolism and host cell homeostasis via inhibition of NMD.
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Affiliation(s)
- Kazumi Nakano
- Laboratory of Tumor Cell Biology, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minatoku, Tokyo, Japan
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88
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An unusual arrangement of two 14-3-3-like domains in the SMG5-SMG7 heterodimer is required for efficient nonsense-mediated mRNA decay. Genes Dev 2013; 27:211-25. [PMID: 23348841 DOI: 10.1101/gad.206672.112] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway triggers the rapid degradation of aberrant mRNAs containing premature translation termination codons (PTCs). In metazoans, NMD requires three 14-3-3-like proteins: SMG5, SMG6, and SMG7. These proteins are recruited to PTC-containing mRNAs through the interaction of their 14-3-3-like domains with phosphorylated UPF1, the central NMD effector. Recruitment of SMG5, SMG6, and SMG7 causes NMD target degradation. In this study, we report the crystal structure of the Caenorhabditis elegans SMG5-SMG7 complex. The 14-3-3-like phosphopeptide recognition domains of SMG5 and SMG7 heterodimerize in an unusual perpendicular back-to-back orientation in which the peptide-binding sites face opposite directions. Structure-based mutants and functional assays indicate that the SMG5-SMG7 interaction is conserved and is crucial for efficient NMD in human cells. Notably, we demonstrate that heterodimerization increases the affinity of the SMG5-SMG7 complex for UPF1. Furthermore, we show that the degradative activity of the SMG5-SMG7 complex resides in SMG7 and that the SMG5-SMG7 complex and SMG6 play partially redundant roles in the degradation of aberrant mRNAs. We propose that the SMG5-SMG7 complex binds to phosphorylated UPF1 with high affinity and recruits decay factors to the mRNA target through SMG7, thus promoting target degradation.
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89
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Schweingruber C, Rufener SC, Zünd D, Yamashita A, Mühlemann O. Nonsense-mediated mRNA decay - mechanisms of substrate mRNA recognition and degradation in mammalian cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:612-23. [PMID: 23435113 DOI: 10.1016/j.bbagrm.2013.02.005] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/10/2013] [Accepted: 02/12/2013] [Indexed: 12/15/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway is well known as a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with truncated open reading frames (ORF) due to the presence of a premature termination codon (PTC). However, a more general role of NMD in posttranscriptional regulation of gene expression is indicated by transcriptome-wide mRNA profilings that identified a plethora of physiological mRNAs as NMD targets. In this review, we focus on mechanistic aspects of target mRNA identification and degradation in mammalian cells, based on the available biochemical and genetic data, and point out knowledge gaps. Translation termination in a messenger ribonucleoprotein particle (mRNP) environment lacking necessary factors for proper translation termination emerges as a key determinant for subjecting an mRNA to NMD, and we therefore review recent structural and mechanistic insight into translation termination. In addition, the central role of UPF1, its crucial phosphorylation/dephosphorylation cycle and dynamic interactions with other NMD factors are discussed. Moreover, we address the role of exon junction complexes (EJCs) in NMD and summarize the functions of SMG5, SMG6 and SMG7 in promoting mRNA decay through different routes. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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90
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Chuang TW, Chang WL, Lee KM, Tarn WY. The RNA-binding protein Y14 inhibits mRNA decapping and modulates processing body formation. Mol Biol Cell 2013; 24:1-13. [PMID: 23115303 PMCID: PMC3530774 DOI: 10.1091/mbc.e12-03-0217] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 10/22/2012] [Accepted: 10/24/2012] [Indexed: 01/12/2023] Open
Abstract
The exon-junction complex (EJC) deposited on a newly spliced mRNA plays an important role in subsequent mRNA metabolic events. Here we show that an EJC core heterodimer, Y14/Magoh, specifically associates with mRNA-degradation factors, including the mRNA-decapping complex and exoribonucleases, whereas another core factor, eIF4AIII/MLN51, does not. We also demonstrate that Y14 interacts directly with the decapping factor Dcp2 and the 5' cap structure of mRNAs via different but overlapping domains and that Y14 inhibits the mRNA-decapping activity of Dcp2 in vitro. Accordingly, overexpression of Y14 prolongs the half-life of a reporter mRNA. Therefore Y14 may function independently of the EJC in preventing mRNA decapping and decay. Furthermore, we observe that depletion of Y14 disrupts the formation of processing bodies, whereas overexpression of a phosphomimetic Y14 considerably increases the number of processing bodies, perhaps by sequestering the mRNA-degradation factors. In conclusion, this report provides unprecedented evidence for a role of Y14 in regulating mRNA degradation and processing body formation and reinforces the influence of phosphorylation of Y14 on its activity in postsplicing mRNA metabolism.
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Affiliation(s)
- Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Wei-Lun Chang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
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91
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Doidge R, Mittal S, Aslam A, Winkler GS. The anti-proliferative activity of BTG/TOB proteins is mediated via the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylase subunits of the Ccr4-not complex. PLoS One 2012; 7:e51331. [PMID: 23236473 PMCID: PMC3517456 DOI: 10.1371/journal.pone.0051331] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/06/2012] [Indexed: 11/19/2022] Open
Abstract
The human BTG/TOB protein family comprises six members (BTG1, BTG2/PC3/Tis21, BTG3/Ana, BTG4/PC3B, TOB1/Tob, and TOB2) that are characterised by a conserved BTG domain. This domain mediates interactions with the highly similar Caf1a (CNOT7) and Caf1b (CNOT8) catalytic subunits of the Ccr4-Not deadenylase complex. BTG/TOB proteins have anti-proliferative activity: knockdown of BTG/TOB can result in increased cell proliferation, whereas over-expression of BTG/TOB leads to inhibition of cell cycle progression. It was unclear whether the interaction between BTG/TOB proteins and the Caf1a/Caf1b deadenylases is necessary for the anti-proliferative activity of BTG/TOB. To address this question, we further characterised surface-exposed amino acid residues of BTG2 and TOB1 that mediate the interaction with the Caf1a and Caf1b deadenylase enzymes. We then analysed the role of BTG2 and TOB1 in the regulation of cell proliferation, translation and mRNA abundance using a mutant that is no longer able to interact with the Caf1a/Caf1b deadenylases. We conclude that the anti-proliferative activity of BTG/TOB proteins is mediated through interactions with the Caf1a and Caf1b deadenylase enzymes. Furthermore, we show that the activity of BTG/TOB proteins in the regulation of mRNA abundance and translation is dependent on Caf1a/Caf1b, and does not appear to require other Ccr4-Not components, including the Ccr4a (CNOT6)/Ccr4b (CNOT6L) deadenylases, or the non-catalytic subunits CNOT1 or CNOT3.
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Affiliation(s)
- Rachel Doidge
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Saloni Mittal
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Akhmed Aslam
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - G. Sebastiaan Winkler
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- * E-mail:
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92
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Nguyen LS, Jolly L, Shoubridge C, Chan WK, Huang L, Laumonnier F, Raynaud M, Hackett A, Field M, Rodriguez J, Srivastava AK, Lee Y, Long R, Addington AM, Rapoport JL, Suren S, Hahn CN, Gamble J, Wilkinson MF, Corbett MA, Gecz J. Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability. Mol Psychiatry 2012; 17:1103-15. [PMID: 22182939 PMCID: PMC4281019 DOI: 10.1038/mp.2011.163] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/27/2011] [Accepted: 10/24/2011] [Indexed: 11/09/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway was originally discovered by virtue of its ability to rapidly degrade aberrant mRNAs with premature termination codons. More recently, it was shown that NMD also directly regulates subsets of normal transcripts, suggesting that NMD has roles in normal biological processes. Indeed, several NMD factors have been shown to regulate neurological events (for example, neurogenesis and synaptic plasticity) in numerous vertebrate species. In man, mutations in the NMD factor gene UPF3B, which disrupts a branch of the NMD pathway, cause various forms of intellectual disability (ID). Using Epstein Barr virus-immortalized B cells, also known as lymphoblastoid cell lines (LCLs), from ID patients that have loss-of-function mutations in UPF3B, we investigated the genome-wide consequences of compromised NMD and the role of NMD in neuronal development and function. We found that ~5% of the human transcriptome is impacted in UPF3B patients. The UPF3B paralog, UPF3A, is stabilized in all UPF3B patients, and partially compensates for the loss of UPF3B function. Interestingly, UPF3A protein, but not mRNA, was stabilised in a quantitative manner that inversely correlated with the severity of patients' phenotype. This suggested that the ability to stabilize the UPF3A protein is a crucial modifier of the neurological symptoms due to loss of UPF3B. We also identified ARHGAP24, which encodes a GTPase-activating protein, as a canonical target of NMD, and we provide evidence that deregulation of this gene inhibits axon and dendrite outgrowth and branching. Our results demonstrate that the UPF3B-dependent NMD pathway is a major regulator of the transcriptome and that its targets have important roles in neuronal cells.
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Affiliation(s)
- LS Nguyen
- Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
- Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia
| | - L Jolly
- Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia
| | - C Shoubridge
- Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
- Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia
| | - WK Chan
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - L Huang
- Department of Reproductive Medicine, University of California, San Diego, CA, USA
| | - F Laumonnier
- INSERM, U930, Tours, France
- CNRS, ERL3106, Tours, France
- University Francois-Rabelais, UMR ‘Imaging and Brain’, Tours, France
| | - M Raynaud
- INSERM, U930, Tours, France
- University Francois-Rabelais, UMR ‘Imaging and Brain’, Tours, France
- CHRU de Tours, Service de Genetique, Tours, France
| | - A Hackett
- GOLD Service, Hunter Genetics, Newcastle, Australia
| | - M Field
- GOLD Service, Hunter Genetics, Newcastle, Australia
| | - J Rodriguez
- J.C. Self Research Institute, Greenwood Genetic Centre, Greenwood, SC, USA
| | - AK Srivastava
- J.C. Self Research Institute, Greenwood Genetic Centre, Greenwood, SC, USA
| | - Y Lee
- Child Psychiatry Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - R Long
- Child Psychiatry Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - AM Addington
- Child Psychiatry Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - JL Rapoport
- Child Psychiatry Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - S Suren
- Human Developmental Biology Resource, Neural Development Unit, UCL Institute of Child Health, London, UK
| | - CN Hahn
- Department of Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
| | - J Gamble
- Centenary Institute of Cancer Medicine & Cell Biology, University of Sydney, NSW, Australia
| | - MF Wilkinson
- Department of Reproductive Medicine, University of California, San Diego, CA, USA
| | - MA Corbett
- Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia
| | - J Gecz
- Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
- Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia
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93
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Nicholson P, Joncourt R, Mühlemann O. Analysis of nonsense-mediated mRNA decay in mammalian cells. CURRENT PROTOCOLS IN CELL BIOLOGY 2012; Chapter 27:Unit27.4. [PMID: 22733442 DOI: 10.1002/0471143030.cb2704s55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway acts to selectively identify and degrade mRNAs that contain a premature translation termination codon (PTC), and hence reduce the accumulation of potentially toxic truncated proteins. NMD is one of the best studied mRNA quality-control mechanisms in eukaryotes, and it has become clear during recent years that many physiological mRNAs are also NMD substrates, signifying a role for NMD beyond mRNA quality control as a translation-dependent post-transcriptional regulator of gene expression. Despite a great deal of scientific research for over twenty years, the process of NMD is far from being fully understood with regard to its physiological relevance to the cell, the molecular mechanisms that underpin this pathway, all of the factors that are involved, and the exact cellular locations of NMD. This unit details some of the fundamental RNA based approaches taken to examine aspects of NMD, such as creating PTC+ reporter genes, knocking down key NMD factors via RNAi, elucidating the important functions of NMD factors by complementation assays or Tethered Function Assays, and measuring RNA levels by reverse-transcription quantitative PCR.
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94
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Inducible control of subcellular RNA localization using a synthetic protein-RNA aptamer interaction. PLoS One 2012; 7:e46868. [PMID: 23056498 PMCID: PMC3466194 DOI: 10.1371/journal.pone.0046868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/05/2012] [Indexed: 12/18/2022] Open
Abstract
Evidence is accumulating in support of the functional importance of subcellular RNA localization in diverse biological contexts. In different cell types, distinct RNA localization patterns are frequently observed, and the available data indicate that this is achieved through a series of highly coordinated events. Classically, cis–elements within the RNA to be localized are recognized by RNA-binding proteins (RBPs), which then direct specific localization of a target RNA. Until now, the precise control of the spatiotemporal parameters inherent to regulating RNA localization has not been experimentally possible. Here, we demonstrate the development and use of a chemically–inducible RNA–protein interaction to regulate subcellular RNA localization. Our system is composed primarily of two parts: (i) the Tet Repressor protein (TetR) genetically fused to proteins natively involved in localizing endogenous transcripts; and (ii) a target transcript containing genetically encoded TetR–binding RNA aptamers. TetR–fusion protein binding to the target RNA and subsequent localization of the latter are directly regulated by doxycycline. Using this platform, we demonstrate that enhanced and controlled subcellular localization of engineered transcripts are achievable. We also analyze rules for forward engineering this RNA localization system in an effort to facilitate its straightforward application to studying RNA localization more generally.
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95
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Huang L, Wilkinson MF. Regulation of nonsense-mediated mRNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:807-28. [PMID: 23027648 DOI: 10.1002/wrna.1137] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved pathway that was originally identified as a RNA surveillance mechanism that degrades aberrant mRNAs harboring premature termination (nonsense) codons. Recently, it was discovered that NMD also regulates normal gene expression. Genome-wide studies showed that ablation of NMD alters the expression of ∼10% of transcripts in a wide variety of eukaryotes. In general, NMD specifically targets normal transcripts that harbor a stop codon in a premature context. The finding that NMD regulates normal gene expression raises the possibility that NMD itself is subject to regulation. Indeed, recent studies have shown that NMD efficiency varies in different cell types and tissues. NMD is also subject to developmental control in both higher and lower eukaryotic species. Molecular mechanisms have been defined-including those involving microRNAs and other RNA decay pathways-that regulate the magnitude of NMD in some developmental settings. This developmental regulation of NMD appears to have physiological roles, at least in some model systems. In addition to mechanisms that modulate the efficiency of NMD, mechanisms have recently been identified that serve the opposite purpose: to maintain the efficiency of NMD in the face of insults. This 'buffering' is achieved by feedback networks that serve to regulate the stability of NMD factors. The discovery of NMD homeostasis and NMD regulatory mechanisms has important implications for how NMD acts in biological processes and how its magnitude could potentially be manipulated for clinical benefit.
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Affiliation(s)
- Lulu Huang
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
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96
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Liu C, Zhang X, Huang F, Yang B, Li J, Liu B, Luo H, Zhang P, Zhang H. APOBEC3G inhibits microRNA-mediated repression of translation by interfering with the interaction between Argonaute-2 and MOV10. J Biol Chem 2012; 287:29373-83. [PMID: 22791714 DOI: 10.1074/jbc.m112.354001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The apolipoprotein-B-mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or A3G) is a potent restrictive factor for human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. It belongs to the cytidine deaminase family. Recent studies have shown that A3G significantly inhibits microRNA (miRNA)-mediated repression of translation. However, the mechanism underlying this action must be clarified. In this report, we have demonstrated that A3G counteracts miRNA-mediated repression of translation by inhibiting the interaction between moloney leukemia virus 10 (MOV10) protein and Argonaute-2 (AGO2), causing either abnormal assembly or abnormal maturation of miRNA-inducing silencing complex (miRISC). Through a series of MOV10 deletions, we found that A3G binds to a domain at the C terminus in MOV10, where it competitively inhibits the binding of AGO2 to that same domain. The interaction between A3G and MOV10 relies on its association with a small RNA named 7SL RNA. The A3G mutant W127L, which is unable to bind to 7SL RNA, shows significantly incapability to counteract the miRNA-mediated repression of translation. Our data demonstrate a novel mechanism involved in the regulation of miRISC activity. Although both A3G and MOV10 belong to the interferon antiviral system and inhibit HIV-1 and other retroviruses, their opposing effects on the cellular miRNA activity suggest that they play much more complicated regulatory roles in various cellular functions.
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Affiliation(s)
- Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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97
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Kim KM, Cho H, Kim YK. The upstream open reading frame of cyclin-dependent kinase inhibitor 1A mRNA negatively regulates translation of the downstream main open reading frame. Biochem Biophys Res Commun 2012; 424:469-75. [PMID: 22771799 DOI: 10.1016/j.bbrc.2012.06.135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 06/26/2012] [Indexed: 12/29/2022]
Abstract
The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein 80 and 20 (CBP80/20). During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here, our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A; also known as Waf1/p21) mRNAs increases in cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is a NMD-inducing feature. Using chimeric reporter constructs, we find that the uORF of CDKN1A mRNA negatively modulates translation of the main downstream ORF. These findings provide biological insights into the possible role of NMD in diverse biological pathways mediated by CDKN1A.
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Affiliation(s)
- Kyoung Mi Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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98
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Shigeoka T, Kato S, Kawaichi M, Ishida Y. Evidence that the Upf1-related molecular motor scans the 3'-UTR to ensure mRNA integrity. Nucleic Acids Res 2012; 40:6887-97. [PMID: 22554850 PMCID: PMC3413143 DOI: 10.1093/nar/gks344] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Upf1 is a highly conserved RNA helicase essential for nonsense-mediated mRNA decay (NMD), an mRNA quality-control mechanism that degrades aberrant mRNAs harboring premature termination codons (PTCs). For the activation of NMD, UPF1 interacts first with a translation–terminating ribosome and then with a downstream exon–junction complex (EJC), which is deposited at exon–exon junctions during splicing. Although the helicase activity of Upf1 is indispensable for NMD, its roles and substrates have yet to be fully elucidated. Here we show that stable RNA secondary structures between a PTC and a downstream exon–exon junction increase the levels of potential NMD substrates. We also demonstrate that a stable secondary structure within the 3′-untranslated region (UTR) induces the binding of Upf1 to mRNA in a translation-dependent manner and that the Upf1-related molecules are accumulated at the 5′-side of such a structure. Furthermore, we present evidence that the helicase activity of Upf1 is used to bridge the spatial gap between a translation–termination codon and a downstream exon–exon junction for the activation of NMD. Based on these findings, we propose a model that the Upf1-related molecular motor scans the 3′-UTR in the 5′-to-3′ direction for the mRNA-binding factors including EJCs to ensure mRNA integrity.
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Affiliation(s)
- Toshiaki Shigeoka
- Division of Gene Function in Animals, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192, Japan
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99
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Lynch SA, Nguyen LS, Ng LY, Waldron M, McDonald D, Gecz J. Broadening the phenotype associated with mutations in UPF3B: two further cases with renal dysplasia and variable developmental delay. Eur J Med Genet 2012; 55:476-9. [PMID: 22609145 DOI: 10.1016/j.ejmg.2012.03.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 03/31/2012] [Indexed: 11/16/2022]
Abstract
We present two brothers with mutations in UPF3B, an X-linked intellectual disability gene. Our family consists of two affected brothers and a carrier mother. Both affected brothers had renal dysplasia. A maternal uncle died from a congenital heart defect at 4 months. The two boys had variable degrees of developmental delay. One had macrocephaly, significant expressive speech delay and constipation. The other brother had normocephaly, obsessional tendencies and was diagnosed with high functioning autism. The phenotypically normal mother had 100% skewed X-inactivation. Our cases expand the phenotype seen with UPF3B mutations and highlight the variability within families.
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Affiliation(s)
- Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland.
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100
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Melero R, Buchwald G, Castaño R, Raabe M, Gil D, Lázaro M, Urlaub H, Conti E, Llorca O. The cryo-EM structure of the UPF-EJC complex shows UPF1 poised toward the RNA 3' end. Nat Struct Mol Biol 2012; 19:498-505, S1-2. [PMID: 22522823 DOI: 10.1038/nsmb.2287] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/22/2012] [Indexed: 11/09/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that degrades aberrant mRNAs containing premature termination codons (PTCs). NMD is triggered upon the assembly of the UPF surveillance complex near a PTC. In humans, UPF assembly is prompted by the exon junction complex (EJC). We investigated the molecular architecture of the human UPF complex bound to the EJC by cryo-EM and using positional restraints from additional EM, MS and biochemical interaction data. The heptameric assembly is built around UPF2, a scaffold protein with a ring structure that closes around the CH domain of UPF1, keeping the helicase region in an accessible and unwinding-competent state. UPF2 also positions UPF3 to interact with the EJC. The geometry is such that this transient complex poises UPF1 to elicit helicase activity toward the 3' end of the mRNP.
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Affiliation(s)
- Roberto Melero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council), Madrid, Spain
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