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Nicholson P, Gkratsou A, Josi C, Colombo M, Mühlemann O. Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells. RNA (NEW YORK, N.Y.) 2018; 24:557-573. [PMID: 29348139 PMCID: PMC5855955 DOI: 10.1261/rna.063719.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
The term "nonsense-mediated mRNA decay" (NMD) originally described the degradation of mRNAs with premature translation-termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3%-10% of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5-SMG7 or SMG5-PNRC2 binding to UPF1. However, the existence, dominance, and mechanistic details of these exonucleolytic pathways are divisive. Therefore, we have investigated the possible exonucleolytic modes of mRNA decay in NMD by examining the roles of UPF1, SMG5, SMG7, and PNRC2 using a combination of functional assays and interaction mapping. Confirming previous work, we detected an interaction between SMG5 and SMG7 and also a functional need for this complex in NMD. In contrast, we found no evidence for the existence of a physical or functional interaction between SMG5 and PNRC2. Instead, we show that UPF1 interacts with PNRC2 and that it triggers 5'-3' exonucleolytic decay of reporter transcripts in tethering assays. PNRC2 interacts mainly with decapping factors and its knockdown does not affect the RNA levels of NMD reporters. We conclude that PNRC2 is probably an important mRNA decapping factor but that it does not appear to be required for NMD.
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Affiliation(s)
- Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Asimina Gkratsou
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Christoph Josi
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
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Haque N, Ouda R, Chen C, Ozato K, Hogg JR. ZFR coordinates crosstalk between RNA decay and transcription in innate immunity. Nat Commun 2018; 9:1145. [PMID: 29559679 PMCID: PMC5861047 DOI: 10.1038/s41467-018-03326-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
Control of type I interferon production is crucial to combat infection while preventing deleterious inflammatory responses, but the extent of the contribution of post-transcriptional mechanisms to innate immune regulation is unclear. Here, we show that human zinc finger RNA-binding protein (ZFR) represses the interferon response by regulating alternative pre-mRNA splicing. ZFR expression is tightly controlled during macrophage development; monocytes express truncated ZFR isoforms, while macrophages induce full-length ZFR to modulate macrophage-specific alternative splicing. Interferon-stimulated genes are constitutively activated by ZFR depletion, and immunostimulation results in hyper-induction of interferon β (IFNβ/IFNB1). Through whole-genome analyses, we show that ZFR controls interferon signaling by preventing aberrant splicing and nonsense-mediated decay of histone variant macroH2A1/H2AFY mRNAs. Together, our data suggest that regulation of ZFR in macrophage differentiation guards against aberrant interferon responses and reveal a network of mRNA processing and decay that shapes the transcriptional response to infection. Type I interferon signaling is critical for the control of infection. Here the authors show that zinc finger RNA-binding protein (ZFR) can control type I interferon responses, and that this control is itself regulated by distinct ZFR truncation patterns that differ between monocytes and macrophages.
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Affiliation(s)
- Nazmul Haque
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Room 2341, Bethesda, MD, 20892, USA.
| | - Ryota Ouda
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - Chao Chen
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Room 2341, Bethesda, MD, 20892, USA.
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103
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Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross JD. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun 2018; 9:1152. [PMID: 29559651 PMCID: PMC5861098 DOI: 10.1038/s41467-018-03536-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/22/2018] [Indexed: 11/17/2022] Open
Abstract
The conserved decapping enzyme Dcp2 recognizes and removes the 5′ eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis. The decapping enzyme Dcp2 removes the 5′ eukaryotic cap from mRNA transcripts and acts in concert with its essential activator Dcp1 and various coactivators. Here the authors present the structure of the fully-activated mRNA decapping complex, which reveals how Dcp2 recognizes the cap substrate and coactivators Edc1 and Edc3 activate catalysis.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.,Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA.
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104
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Baird TD, Cheng KCC, Chen YC, Buehler E, Martin SE, Inglese J, Hogg JR. ICE1 promotes the link between splicing and nonsense-mediated mRNA decay. eLife 2018. [PMID: 29528287 PMCID: PMC5896957 DOI: 10.7554/elife.33178] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway detects aberrant transcripts containing premature termination codons (PTCs) and regulates expression of 5–10% of non-aberrant human mRNAs. To date, most proteins involved in NMD have been identified by genetic screens in model organisms; however, the increased complexity of gene expression regulation in human cells suggests that additional proteins may participate in the human NMD pathway. To identify proteins required for NMD, we performed a genome-wide RNAi screen against >21,000 genes. Canonical members of the NMD pathway were highly enriched as top hits in the siRNA screen, along with numerous candidate NMD factors, including the conserved ICE1/KIAA0947 protein. RNAseq studies reveal that depletion of ICE1 globally enhances accumulation and stability of NMD-target mRNAs. Further, our data suggest that ICE1 uses a putative MIF4G domain to interact with exon junction complex (EJC) proteins and promotes the association of the NMD protein UPF3B with the EJC. The DNA in our cells contains the hereditary information that makes each of us unique. Molecules called mRNAs are copies of this information and are used as templates for making proteins. When a strand of incorrectly copied mRNA, or one including errors from the original DNA template, is recognized, our cells destroy the mRNA to prevent it from producing a damaged protein. Organisms from yeast to humans have evolved a mechanism for finding and destroying faulty mRNAs, called mRNA surveillance. Animals are particularly reliant on mRNA surveillance, as their proteins are often made from cutting and pasting together mRNA from different portions of DNA, in a process known as splicing. Despite being a vital process, we still lack a good understanding of how mRNA surveillance works. Now, Baird et al. used human kidney cells that produced an error-containing mRNA that could be tracked. To investigate how efficient RNA surveillance is under different conditions, the levels of individual proteins were reduced one at a time. By tracking the amount of faulty mRNA, it was possible to find out if a single protein plays a role in human mRNA surveillance. If the number of faulty mRNAs is high when a protein is reduced, it suggests that this protein may be involved in mRNA surveillance. Baird et al. screened more than 21,000 proteins, the majority of proteins made in human cells. Many of the proteins that stood out as important in mRNA surveillance were the ones already known to be relevant in yeast and worm cells. But the experiments also identified new proteins that appear to play a role specifically in human RNA surveillance. One of the proteins, ICE1, is essential for the relationship between mRNA splicing and mRNA surveillance. Without ICE1, the mRNA surveillance machinery can no longer find and destroy faulty mRNAs. Nearly one-third of genetic diseases are caused by mutations that result in faulty mRNAs, which can be detected by mRNA surveillance pathways. Depending on the disease, destroying these error-containing mRNAs can either improve or worsen disease symptoms. A better understanding of the factors that control human RNA surveillance could one day help to develop treatments that affect mRNA surveillance to improve disease outcomes.
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Affiliation(s)
- Thomas D Baird
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Yu-Chi Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Eugen Buehler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - Scott E Martin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, United States
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
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105
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Beyond quality control: The role of nonsense-mediated mRNA decay (NMD) in regulating gene expression. Semin Cell Dev Biol 2018; 75:78-87. [DOI: 10.1016/j.semcdb.2017.08.053] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/23/2022]
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106
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Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line. Sci Rep 2018; 8:2628. [PMID: 29422612 PMCID: PMC5805679 DOI: 10.1038/s41598-018-20518-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/18/2018] [Indexed: 01/12/2023] Open
Abstract
Expression of the RNA-binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis compared to other hematopoietic lineages. Csde1 expression is impaired in the severe congenital anemia Diamond Blackfan Anemia (DBA), and reduced expression of Csde1 in healthy erythroblasts impaired their proliferation and differentiation. To investigate the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1 in erythroid cells. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. For instance, protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced indicating more efficient translation of Pabpc1 followed by negative feedback on mRNA stability. Overall, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. Clones with complete loss of Csde1, however, could not be generated. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression.
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107
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Yilmaz S, Uludağ Alkaya D, Kasapçopur Ö, Barut K, Akdemir ES, Celen C, Youngblood MW, Yasuno K, Bilguvar K, Günel M, Tüysüz B. Genotype-phenotype investigation of 35 patients from 11 unrelated families with camptodactyly-arthropathy-coxa vara-pericarditis (CACP) syndrome. Mol Genet Genomic Med 2018; 6:230-248. [PMID: 29397575 PMCID: PMC5902402 DOI: 10.1002/mgg3.364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/12/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
Background The camptodactyly–arthropathy–coxa vara–pericarditis syndrome (CACP) is a rare autosomal recessive condition characterized by camptodactyly, noninflammatory arthropathy, coxa vara, and pericarditis. CACP is caused by mutations in the proteoglycan 4 (PRG4) gene, which encodes a lubricating glycoprotein present in the synovial fluid and at the surface of articular cartilage. Methods In the present study, we compared the clinical and molecular findings of CACP syndrome in 35 patients from 11 unrelated families. In 28 patients, whole exome sequencing was used to investigate genomic variations. Results We found that camptodactyly of hands was the first symptom presented by most patients. Swelling of wrists, knees, and elbows began before 4 years of age, while the age of joint involvement was variable. Patients reported an increased pain level after the age of 10, and severe hip involvement developed after 20 years old. All patients presented developmental coxa vara and seven patients (~22%) had pleural effusion, pericarditis, and/or ascites. We identified nine novel genomic alterations, including the first case of homozygous complete deletion of exon 1 in the PRG4 gene. Conclusion With this study, we contribute to the catalog of CACP causing variants. We confirm that the skeletal component of this disease worsens with age, and presents the potential mechanisms for interfamily variability, by discussing the influence of a modifier gene and escape from nonsense‐mediated mRNA decay. We believe that this report will increase awareness of this familial arthropathic condition and the characteristic clinical and radiological findings will facilitate the differentiation from the common childhood rheumatic diseases such as juvenile idiopathic arthritis.
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Affiliation(s)
- Saliha Yilmaz
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Özgür Kasapçopur
- Department of Pediatric Rheumatology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Kenan Barut
- Department of Pediatric Rheumatology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Ekin S Akdemir
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Cemre Celen
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Mark W Youngblood
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Katsuhito Yasuno
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Murat Günel
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
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108
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HTLV-1 Tax plugs and freezes UPF1 helicase leading to nonsense-mediated mRNA decay inhibition. Nat Commun 2018; 9:431. [PMID: 29382845 PMCID: PMC5789848 DOI: 10.1038/s41467-017-02793-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 12/28/2017] [Indexed: 12/19/2022] Open
Abstract
Up-Frameshift Suppressor 1 Homolog (UPF1) is a key factor for nonsense-mediated mRNA decay (NMD), a cellular process that can actively degrade mRNAs. Here, we study NMD inhibition during infection by human T-cell lymphotropic virus type I (HTLV-1) and characterise the influence of the retroviral Tax factor on UPF1 activity. Tax interacts with the central helicase core domain of UPF1 and might plug the RNA channel of UPF1, reducing its affinity for nucleic acids. Furthermore, using a single-molecule approach, we show that the sequential interaction of Tax with a RNA-bound UPF1 freezes UPF1: this latter is less sensitive to the presence of ATP and shows translocation defects, highlighting the importance of this feature for NMD. These mechanistic insights reveal how HTLV-1 hijacks the central component of NMD to ensure expression of its own genome. UPF1 is a central protein in nonsense-mediated mRNA decay (NMD), but contribution of its RNA processivity to NMD is unclear. Here, the authors show how the retroviral Tax protein interacts with and inhibits UPF1, and demonstrate that UPF1’s translocase activity contributes to NMD.
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109
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Abstract
In mammals, cap-dependent translation of mRNAs is initiated by two distinct mechanisms: cap-binding complex (CBC; a heterodimer of CBP80 and 20)-dependent translation (CT) and eIF4E-dependent translation (ET). Both translation initiation mechanisms share common features in driving cap-dependent translation; nevertheless, they can be distinguished from each other based on their molecular features and biological roles. CT is largely associated with mRNA surveillance such as nonsense-mediated mRNA decay (NMD), whereas ET is predominantly involved in the bulk of protein synthesis. However, several recent studies have demonstrated that CT and ET have similar roles in protein synthesis and mRNA surveillance. In a subset of mRNAs, CT preferentially drives the cap-dependent translation, as ET does, and ET is responsible for mRNA surveillance, as CT does. In this review, we summarize and compare the molecular features of CT and ET with a focus on the emerging roles of CT in translation.
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Affiliation(s)
- Incheol Ryu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841,
Korea
- School of Life Sciences, Korea University, Seoul 02841,
Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841,
Korea
- School of Life Sciences, Korea University, Seoul 02841,
Korea
- Corresponding author. Tel: +82-2-3290-3410; Fax: +82-2-923-9923; E-mail:
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110
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Lejeune F. Nonsense-mediated mRNA decay at the crossroads of many cellular pathways. BMB Rep 2018; 50:175-185. [PMID: 28115040 PMCID: PMC5437961 DOI: 10.5483/bmbrep.2017.50.4.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism ensuring the fast decay of mRNAs harboring a premature termination codon (PTC). As a quality control mechanism, NMD distinguishes PTCs from normal termination codons in order to degrade PTC-carrying mRNAs only. For this, NMD is connected to various other cell processes which regulate or activate it under specific cell conditions or in response to mutations, mis-regulations, stresses, or particular cell programs. These cell processes and their connections with NMD are the focus of this review, which aims both to illustrate the complexity of the NMD mechanism and its regulation and to highlight the cellular consequences of NMD inhibition.
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Affiliation(s)
- Fabrice Lejeune
- University Lille, UMR8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies; CNRS, UMR 8161, 3Institut Pasteur de Lille, F-59000 Lille, France
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111
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Huang L, Low A, Damle SS, Keenan MM, Kuntz S, Murray SF, Monia BP, Guo S. Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations. Genome Biol 2018; 19:4. [PMID: 29334995 PMCID: PMC5769327 DOI: 10.1186/s13059-017-1386-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/29/2017] [Indexed: 01/08/2023] Open
Abstract
Background About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncated proteins, but also often result in decreased mRNA abundance due to nonsense-mediated mRNA decay (NMD). Although pharmacological inhibition of NMD could be an attractive therapeutic approach for the treatment of diseases caused by nonsense mutations, NMD also regulates the expression of 10–20% of the normal transcriptome. Results Here, we investigate whether NMD can be inhibited to stabilize mutant mRNAs, which may subsequently produce functional proteins, without having a major impact on the normal transcriptome. We develop antisense oligonucleotides (ASOs) to systematically deplete each component in the NMD pathway. We find that ASO-mediated depletion of each NMD factor elicits different magnitudes of NMD inhibition in vitro and are differentially tolerated in normal mice. Among all of the NMD factors, Upf3b depletion is well tolerated, consistent with previous reports that UPF3B is not essential for development and regulates only a subset of the endogenous NMD substrates. While minimally impacting the normal transcriptome, Upf3b-ASO treatment significantly stabilizes the PTC-containing dystrophin mRNA in mdx mice and coagulation factor IX mRNA in a hemophilia mouse model. Furthermore, when combined with reagents promoting translational read-through, Upf3b-ASO treatment leads to the production of functional factor IX protein in hemophilia mice. Conclusions These data demonstrate that ASO-mediated reduction of the NMD factor Upf3b could be an effective and safe approach for the treatment of diseases caused by nonsense mutations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1386-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lulu Huang
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Audrey Low
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Sagar S Damle
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | - Steven Kuntz
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | - Brett P Monia
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA.
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112
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Abstract
Cellular mRNA levels are determined by the competing forces of transcription and decay. A wide array of cellular mRNA decay pathways carry out RNA turnover either on a constitutive basis or in response to changing cellular conditions. Here, we outline a method to investigate mRNA decay that employs RNAi knockdown of known or putative decay factors in commercially available Tet-off cell systems. Reporter mRNAs of interest are expressed under the control of a tetracycline-regulated promoter, allowing pulse-chase mRNA decay assays to be conducted. Levels of reporter and constitutively expressed control RNAs throughout the decay assay time course are detected by traditional northern blot analysis and used to calculate mRNA half-lives. We describe the utility of this approach to study nonsense-mediated mRNA decay substrates and factors, but it can be readily adapted to investigate key mechanistic features that dictate the specificity and functions of any mRNA decay pathway.
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Affiliation(s)
- Thomas D Baird
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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113
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Gupta P, Li YR. Upf proteins: highly conserved factors involved in nonsense mRNA mediated decay. Mol Biol Rep 2017; 45:39-55. [PMID: 29282598 DOI: 10.1007/s11033-017-4139-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/14/2017] [Indexed: 11/28/2022]
Abstract
Over 10% of genetic diseases are caused by mutations that introduce a premature termination codon in protein-coding mRNA. Nonsense-mediated mRNA decay (NMD) is an essential cellular pathway that degrades these mRNAs to prevent the accumulation of harmful partial protein products. NMD machinery is also increasingly appreciated to play a role in other essential cellular functions, including telomere homeostasis and the regulation of normal mRNA turnover, and is misregulated in numerous cancers. Hence, understanding and designing therapeutics targeting NMD is an important goal in biomedical science. The central regulator of NMD, the Upf1 protein, interacts with translation termination factors and contextual factors to initiate NMD specifically on mRNAs containing PTCs. The molecular details of how these contextual factors affect Upf1 function remain poorly understood. Here, we review plausible models for the NMD pathway and the evidence for the variety of roles NMD machinery may play in different cellular processes.
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Affiliation(s)
- Puneet Gupta
- Harvard College, Harvard University, Cambridge, MA, 02138, USA.,School of Arts and Sciences, St. Bonaventure University, St. Bonaventure, NY, 14778, USA
| | - Yan-Ruide Li
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA. .,College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China.
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114
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Wang DO, Ninomiya K, Mori C, Koyama A, Haan M, Kitabatake M, Hagiwara M, Chida K, Takahashi SI, Ohno M, Kataoka N. Transport Granules Bound with Nuclear Cap Binding Protein and Exon Junction Complex Are Associated with Microtubules and Spatially Separated from eIF4E Granules and P Bodies in Human Neuronal Processes. Front Mol Biosci 2017; 4:93. [PMID: 29312956 PMCID: PMC5744441 DOI: 10.3389/fmolb.2017.00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/15/2017] [Indexed: 02/05/2023] Open
Abstract
RNA transport and regulated local translation play critically important roles in spatially restricting gene expression in neurons. Heterogeneous population of RNA granules serve as motile units to translocate, store, translate, and degrade mRNAs in the dendrites contain cis-elements and trans-acting factors such as RNA-binding proteins and microRNAs to convey stimulus-, transcript-specific local translation. Here we report a class of mRNA granules in human neuronal processes that are enriched in the nuclear cap-binding protein complex (CBC) and exon junction complex (EJC) core components, Y14 and eIF4AIII. These granules are physically associated with stabilized microtubules and are spatially segregated from eIF4E-enriched granules and P-bodies. The existence of mRNAs retaining both nuclear cap binding protein and EJC in the distal sites of neuronal processes suggests that some localized mRNAs have not yet undergone the “very first translation,” which contribute to the spatio-temporal regulation of gene expression.
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Affiliation(s)
- Dan O Wang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan.,K-CONNEX (Keihanshin Consortium for Fostering Next Generation of Global Leaders in Research), Kyoto, Japan
| | - Kensuke Ninomiya
- Institute for Virus research, Kyoto University, Kyoto, Japan.,Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan
| | - Chihiro Mori
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Ayako Koyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Martine Haan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | | | - Masatoshi Hagiwara
- Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan
| | - Kazuhiro Chida
- Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kyoto, Japan
| | - Shin-Ichiro Takahashi
- Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kyoto, Japan
| | - Mutsuhito Ohno
- Institute for Virus research, Kyoto University, Kyoto, Japan
| | - Naoyuki Kataoka
- Institute for Virus research, Kyoto University, Kyoto, Japan.,Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan.,Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kyoto, Japan.,Medical Innovation Center, Laboratory for Malignancy Control Research, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Medical Top Track Program, Medical Research Institute, Tokyo Dental and Medical University, Tokyo, Japan
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115
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Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA turnover pathway that has been subject to intense scrutiny. NMD identifies and degrades subsets of normal RNAs, as well as abnormal mRNAs containing premature termination codons. A core factor in this pathway—UPF3B—is an adaptor protein that serves as an NMD amplifier and an NMD branch-specific factor. UPF3B is encoded by an X-linked gene that when mutated causes intellectual disability and is associated with neurodevelopmental disorders, including schizophrenia and autism. Neu-Yilik
et al. now report a new function for UPF3B: it modulates translation termination. Using a fully reconstituted
in vitro translation system, they find that UPF3B has two roles in translation termination. First, UPF3B delays translation termination under conditions that mimic premature translation termination. This could drive more efficient RNA decay by allowing more time for the formation of RNA decay-stimulating complexes. Second, UPF3B promotes the dissociation of post-termination ribosomal complexes that lack nascent peptide. This implies that UPF3B could promote ribosome recycling. Importantly, the authors found that UPF3B directly interacts with both RNA and the factors that recognize stop codons—eukaryotic release factors (eRFs)—suggesting that UPF3B serves as a direct regulator of translation termination. In contrast, a NMD factor previously thought to have a central regulatory role in translation termination—the RNA helicase UPF1—was found to indirectly interact with eRFs and appears to act exclusively in post-translation termination events, such as RNA decay, at least
in vitro. The finding that an RNA decay-promoting factor, UFP3B, modulates translation termination has many implications. For example, the ability of UPF3B to influence the development and function of the central nervous system may be not only through its ability to degrade specific RNAs but also through its impact on translation termination and subsequent events, such as ribosome recycling.
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Affiliation(s)
- Zhaofeng Gao
- Department of Reproductive Medicine, University of California San Diego Medical Center, La Jolla, CA, USA
| | - Miles Wilkinson
- Department of Reproductive Medicine, University of California San Diego Medical Center, La Jolla, CA, USA
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116
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Qu YJ, Ge L, Bai JL, Cao YY, Jin YW, Wang H, Yang L, Song F. p.Val19Glyfs*21 and p.Leu228* variants in the survival of motor neuron 1 trigger nonsense-mediated mRNA decay causing the SMN1 PTC+ transcripts degradation. Mutat Res 2017; 806:31-38. [PMID: 28950212 DOI: 10.1016/j.mrfmmm.2017.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/24/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
Spinal Muscular Atrophy (SMA) results from loss-of-function mutations in the survival of motor neuron 1 (SMN1) gene. Our previous research showed that 40% of variants were nonsense or frameshift variants and SMN1 mRNA levels in the patients carrying these variants were significantly decreased. Here we selected one rare variant (p.Val19Glyfs*21) and one common variant (p.Leu228*) to explore the degradation mechanism of mutant transcripts. The levels of full-length (FL)-SMN1 transcripts and SMN protein in the cell lines from the patients with these variants were both significantly reduced (p<0.01). Treatment with two translation inhibitors (puromycin and Cycloheximide (CHX)) markedly increased the levels of FL-SMN1 transcripts with premature translation termination codons (PTCs) (p<0.01) and showed time-dependent (10h>5.5h) but not dose-dependent effects. Moreover, the knockdown of UPF1, a key factor in nonsense-mediated mRNA decay (NMD) by lentivirus, led to a 3.1-fold increase (p<0.01) in FL-SMN1 transcript levels in patient fibroblasts. Our research provides evidence that these two PTC-generating variants (p.Val19Glyfs*21 and p.Leu228*) can trigger NMD, causing rapid degradation of SMN1 transcripts thereby resulting in SMN protein deficiency. These two variants are highly pathogenic and are associated with more severe SMA phenotypes. Varying NMD efficiency after treatment with puromycin and CHX in different cell types was also observed.
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Affiliation(s)
- Yu-Jin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Lin Ge
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jin-Li Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Yan-Yan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Yu-Wei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Lan Yang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
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117
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Causier B, Li Z, De Smet R, Lloyd JPB, Van de Peer Y, Davies B. Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution. Sci Rep 2017; 7:16692. [PMID: 29192227 PMCID: PMC5709506 DOI: 10.1038/s41598-017-16942-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/13/2017] [Indexed: 11/15/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is an essential eukaryotic process regulating transcript quality and abundance, and is involved in diverse processes including brain development and plant defenses. Although some of the NMD machinery is conserved between kingdoms, little is known about its evolution. Phosphorylation of the core NMD component UPF1 is critical for NMD and is regulated in mammals by the SURF complex (UPF1, SMG1 kinase, SMG8, SMG9 and eukaryotic release factors). However, since SMG1 is reportedly missing from the genomes of fungi and the plant Arabidopsis thaliana, it remains unclear how UPF1 is activated outside the metazoa. We used comparative genomics to determine the conservation of the NMD pathway across eukaryotic evolution. We show that SURF components are present in all major eukaryotic lineages, including fungi, suggesting that in addition to UPF1 and SMG1, SMG8 and SMG9 also existed in the last eukaryotic common ancestor, 1.8 billion years ago. However, despite the ancient origins of the SURF complex, we also found that SURF factors have been independently lost across the Eukarya, pointing to genetic buffering within the essential NMD pathway. We infer an ancient role for SURF in regulating UPF1, and the intriguing possibility of undiscovered NMD regulatory pathways.
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Affiliation(s)
- Barry Causier
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium
| | - Riet De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium
| | - James P B Lloyd
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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118
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Reber S, Mechtersheimer J, Nasif S, Benitez JA, Colombo M, Domanski M, Jutzi D, Hedlund E, Ruepp MD. CRISPR-Trap: a clean approach for the generation of gene knockouts and gene replacements in human cells. Mol Biol Cell 2017; 29:75-83. [PMID: 29167381 PMCID: PMC5909934 DOI: 10.1091/mbc.e17-05-0288] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 01/08/2023] Open
Abstract
CRISPR/Cas9-based genome editing offers the possibility to knock out almost any gene of interest in an affordable and simple manner. The most common strategy is the introduction of a frameshift into the open reading frame (ORF) of the target gene which truncates the coding sequence (CDS) and targets the corresponding transcript for degradation by nonsense-mediated mRNA decay (NMD). However, we show that transcripts containing premature termination codons (PTCs) are not always degraded efficiently and can generate C-terminally truncated proteins which might have residual or dominant negative functions. Therefore, we recommend an alternative approach for knocking out genes, which combines CRISPR/Cas9 with gene traps (CRISPR-Trap) and is applicable to ∼50% of all spliced human protein-coding genes and a large subset of lncRNAs. CRISPR-Trap completely prevents the expression of the ORF and avoids expression of C-terminal truncated proteins. We demonstrate the feasibility of CRISPR-Trap by utilizing it to knock out several genes in different human cell lines. Finally, we also show that this approach can be used to efficiently generate gene replacements allowing for modulation of protein levels for otherwise lethal knockouts (KOs). Thus, CRISPR-Trap offers several advantages over conventional KO approaches and allows for generation of clean CRISPR/Cas9-based KOs.
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Affiliation(s)
- Stefan Reber
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Jonas Mechtersheimer
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Sofia Nasif
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | | | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Michal Domanski
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Daniel Jutzi
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet,171 77 Stockholm, Sweden
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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119
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Optimized approach for the identification of highly efficient correctors of nonsense mutations in human diseases. PLoS One 2017; 12:e0187930. [PMID: 29131862 PMCID: PMC5683606 DOI: 10.1371/journal.pone.0187930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/27/2017] [Indexed: 11/23/2022] Open
Abstract
About 10% of patients with a genetic disease carry a nonsense mutation causing their pathology. A strategy for correcting nonsense mutations is premature termination codon (PTC) readthrough, i.e. incorporation of an amino acid at the PTC position during translation. PTC-readthrough-activating molecules appear as promising therapeutic tools for these patients. Unfortunately, the molecules shown to induce PTC readthrough show low efficacy, probably because the mRNAs carrying a nonsense mutation are scarce, as they are also substrates of the quality control mechanism called nonsense-mediated mRNA decay (NMD). The screening systems previously developed to identify readthrough-promoting molecules used cDNA constructs encoding mRNAs immune to NMD. As the molecules identified were not selected for the ability to correct nonsense mutations on NMD-prone PTC-mRNAs, they could be unsuitable for the context of nonsense-mutation-linked human pathologies. Here, a screening system based on an NMD-prone mRNA is described. It should be suitable for identifying molecules capable of efficiently rescuing the expression of human genes harboring a nonsense mutation. This system should favor the discovery of candidate drugs for treating genetic diseases caused by nonsense mutations. One hit selected with this screening system is presented and validated on cells from three cystic fibrosis patients.
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120
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Lehtiniemi T, Kotaja N. Germ granule-mediated RNA regulation in male germ cells. Reproduction 2017; 155:R77-R91. [PMID: 29038333 DOI: 10.1530/rep-17-0356] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/09/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022]
Abstract
Germ cells have exceptionally diverse transcriptomes. Furthermore, the progress of spermatogenesis is accompanied by dramatic changes in gene expression patterns, the most drastic of them being near-to-complete transcriptional silencing during the final steps of differentiation. Therefore, accurate RNA regulatory mechanisms are critical for normal spermatogenesis. Cytoplasmic germ cell-specific ribonucleoprotein (RNP) granules, known as germ granules, participate in posttranscriptional regulation in developing male germ cells. Particularly, germ granules provide platforms for the PIWI-interacting RNA (piRNA) pathway and appear to be involved both in piRNA biogenesis and piRNA-targeted RNA degradation. Recently, other RNA regulatory mechanisms, such as the nonsense-mediated mRNA decay pathway have also been associated to germ granules providing new exciting insights into the function of germ granules. In this review article, we will summarize our current knowledge on the role of germ granules in the control of mammalian male germ cell's transcriptome and in the maintenance of fertility.
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Affiliation(s)
| | - Noora Kotaja
- Institute of BiomedicineUniversity of Turku, Turku, Finland
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121
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Fujita S, Kuroda Y, Fukui K, Iwamoto R, Kozawa J, Watanabe T, Yamada Y, Imagawa A, Iwahashi H, Shimomura I. Hyperinsulinemia and Insulin Receptor Gene Mutation in Nonobese Healthy Subjects in Japan. J Endocr Soc 2017; 1:1351-1361. [PMID: 29264459 PMCID: PMC5686598 DOI: 10.1210/js.2017-00332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/09/2017] [Indexed: 11/22/2022] Open
Abstract
Context: Hyperinsulinemia is often observed in obese people, owing to their insulin resistance accompanied by visceral fat accumulation, but the frequency of hyperinsulinemia in nonobese people is not well known. Mutations in the insulin receptor gene are known to cause insulin resistance and hyperinsulinemia in type A insulin resistance syndrome, Rabson-Mendenhall syndrome, and Donohue syndrome. However, insulin receptor gene abnormalities have not been investigated in asymptomatic hyperinsulinemic subjects. Purpose: The aim of the current study was to investigate the prevalence of hyperinsulinemia in nonobese Japanese subjects and to examine the involvement of insulin receptor gene mutations. Methods: We enrolled 11,046 subjects who received health checkups. From these, we extracted nonobese subjects (body mass index <25 kg/m2) who exhibited hyperinsulinemia (serum fasting immunoreactive insulin ≥15 µU/mL). Genetic analysis was performed for the insulin receptor gene in 11 nonobese subjects with hyperinsulinemia. Results: The prevalence of hyperinsulinemia without apparent diabetes in nonobese subjects was 0.4% (33/8630). In the 11 analyzed subjects, two novel heterozygous nonsense mutations were detected [c.2106 T>G (p.Y702X) and c.2779-2780 GC>A]. The prevalence of insulin receptor gene mutations was 18.2% (2/11). Conclusions: To our knowledge, this is the first report of the prevalence of hyperinsulinemia in nonobese healthy subjects. We identified two novel mutations in the insulin receptor gene. These findings indicate that mutations in the insulin receptor gene may be related to fasting hyperinsulinemia, and insulin receptor gene screening may be useful for determining the cause of unexplained hyperinsulinemia.
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Affiliation(s)
- Shingo Fujita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yohei Kuroda
- Department of Endocrinology and Metabolism, Sumitomo Hospital, Osaka, 530-0005, Japan
| | - Kenji Fukui
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Ryuya Iwamoto
- Department of Endocrinology and Metabolism, Sumitomo Hospital, Osaka, 530-0005, Japan
| | - Junji Kozawa
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | | | - Yuya Yamada
- Department of Endocrinology and Metabolism, Sumitomo Hospital, Osaka, 530-0005, Japan
| | - Akihisa Imagawa
- Department of Internal Medicine (I), Osaka Medical College, Osaka, 569-8686, Japan
| | - Hiromi Iwahashi
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.,Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
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122
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Proskorovski-Ohayon R, Kadir R, Michalowski A, Flusser H, Perez Y, Hershkovitz E, Sivan S, Birk OS. PAX7mutation in a syndrome of failure to thrive, hypotonia, and global neurodevelopmental delay. Hum Mutat 2017; 38:1671-1683. [DOI: 10.1002/humu.23310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/16/2017] [Accepted: 07/27/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Regina Proskorovski-Ohayon
- The Morris Kahn Laboratory of Human Genetics; National Institute for Biotechnology in the Negev and Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Rotem Kadir
- The Morris Kahn Laboratory of Human Genetics; National Institute for Biotechnology in the Negev and Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Analia Michalowski
- Zussman Child Development Center; Division of Pediatrics; Soroka University Medical Center; Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Hagit Flusser
- Zussman Child Development Center; Division of Pediatrics; Soroka University Medical Center; Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics; National Institute for Biotechnology in the Negev and Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Eli Hershkovitz
- Pediatric Endocrinology and Metabolism Unit; Division of Pediatrics; Soroka University Medical Center; Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Sara Sivan
- The Morris Kahn Laboratory of Human Genetics; National Institute for Biotechnology in the Negev and Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Ohad S. Birk
- The Morris Kahn Laboratory of Human Genetics; National Institute for Biotechnology in the Negev and Faculty of Health Sciences; Ben Gurion University of the Negev; Beer Sheva Israel
- Genetics Institute; Soroka University Medical Center; affiliated to Ben Gurion University of the Negev; Beer Sheva Israel
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123
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Neu-Yilik G, Raimondeau E, Eliseev B, Yeramala L, Amthor B, Deniaud A, Huard K, Kerschgens K, Hentze MW, Schaffitzel C, Kulozik AE. Dual function of UPF3B in early and late translation termination. EMBO J 2017; 36:2968-2986. [PMID: 28899899 PMCID: PMC5641913 DOI: 10.15252/embj.201797079] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/09/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that recognizes and degrades mRNAs with premature termination codons (PTCs). The mechanisms underlying translation termination are key to the understanding of RNA surveillance mechanisms such as NMD and crucial for the development of therapeutic strategies for NMD-related diseases. Here, we have used a fully reconstituted in vitro translation system to probe the NMD proteins for interaction with the termination apparatus. We discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post-termination ribosomal complexes that are devoid of the nascent peptide. Furthermore, we identified UPF1 and ribosomes as new interaction partners of UPF3B. These previously unknown functions of UPF3B during the early and late phases of translation termination suggest that UPF3B is involved in the crosstalk between the NMD machinery and the PTC-bound ribosome, a central mechanistic step of RNA surveillance.
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Affiliation(s)
- Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Hopp Kindertumorzentrum am NCT Heidelberg, Heidelberg, Germany
| | | | - Boris Eliseev
- European Molecular Biology Laboratory, Grenoble, France
| | | | - Beate Amthor
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Karine Huard
- European Molecular Biology Laboratory, Grenoble, France
| | - Kathrin Kerschgens
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany .,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble, France .,School of Biochemistry, University of Bristol, Bristol, UK
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany .,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Hopp Kindertumorzentrum am NCT Heidelberg, Heidelberg, Germany
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124
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Jia J, Werkmeister E, Gonzalez-Hilarion S, Leroy C, Gruenert DC, Lafont F, Tulasne D, Lejeune F. Premature termination codon readthrough in human cells occurs in novel cytoplasmic foci and requires UPF proteins. J Cell Sci 2017; 130:3009-3022. [PMID: 28743738 DOI: 10.1242/jcs.198176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 07/13/2017] [Indexed: 01/01/2023] Open
Abstract
Nonsense-mutation-containing messenger ribonucleoprotein particles (mRNPs) transit through cytoplasmic foci called P-bodies before undergoing nonsense-mediated mRNA decay (NMD), a cytoplasmic mRNA surveillance mechanism. This study shows that the cytoskeleton modulates transport of nonsense-mutation-containing mRNPs to and from P-bodies. Impairing the integrity of cytoskeleton causes inhibition of NMD. The cytoskeleton thus plays a crucial role in NMD. Interestingly, disruption of actin filaments results in both inhibition of NMD and activation of premature termination codon (PTC) readthrough, while disruption of microtubules causes only NMD inhibition. Activation of PTC readthrough occurs concomitantly with the appearance of cytoplasmic foci containing UPF proteins and mRNAs with nonsense mutations but lacking the P-body marker DCP1a. These findings demonstrate that in human cells, PTC readthrough occurs in novel 'readthrough bodies' and requires the presence of UPF proteins.
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Affiliation(s)
- Jieshuang Jia
- Univ. Lille, UMR8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, 59000 Lille, France.,CNRS, UMR 8161, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Elisabeth Werkmeister
- Institut Pasteur de Lille, 59000 Lille, France.,Cellular Microbiology and Physics of Infection group - Center for Infection and Immunity of Lille, Univ. Lille, 59019 Lille, France.,CNRS, UMR8204, 59019 Lille, France.,Inserm, U1019, 59019 Lille, France.,CHU de Lille, 59000 Lille, France
| | | | - Catherine Leroy
- Univ. Lille, UMR8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, 59000 Lille, France.,CNRS, UMR 8161, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Dieter C Gruenert
- Department of Otolaryngology-Head and Neck Surgery, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Pediatrics, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Frank Lafont
- CNRS, UMR8204, 59019 Lille, France.,Inserm, U1019, 59019 Lille, France.,CHU de Lille, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - David Tulasne
- Univ. Lille, UMR8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, 59000 Lille, France.,CNRS, UMR 8161, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, UMR8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, 59000 Lille, France .,CNRS, UMR 8161, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
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125
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Elbarbary RA, Miyoshi K, Hedaya O, Myers JR, Maquat LE. UPF1 helicase promotes TSN-mediated miRNA decay. Genes Dev 2017; 31:1483-1493. [PMID: 28827400 PMCID: PMC5588929 DOI: 10.1101/gad.303537.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022]
Abstract
While microRNAs (miRNAs) regulate the vast majority of protein-encoding transcripts, little is known about how miRNAs themselves are degraded. We recently described Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay (TumiD) as a cellular pathway in which the nuclease TSN promotes the decay of miRNAs that contain CA and/or UA dinucleotides. While TSN-mediated degradation of either protein-free or AGO2-loaded miRNAs does not require the ATP-dependent RNA helicase UPF1 in vitro, we report here that cellular TumiD requires UPF1. Results from experiments using AGO2-loaded miRNAs in duplex with target mRNAs indicate that UPF1 can dissociate miRNAs from their mRNA targets, making the miRNAs susceptible to TumiD. miR-seq (deep sequencing of miRNAs) data reveal that the degradation of ∼50% of candidate TumiD targets in T24 human urinary bladder cancer cells is augmented by UPF1. We illustrate the physiological relevance by demonstrating that UPF1-augmented TumiD promotes the invasion of T24 cells in part by degrading anti-invasive miRNAs so as to up-regulate the expression of proinvasive proteins.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Keita Miyoshi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Omar Hedaya
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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126
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Li L, Lingaraju M, Basquin C, Basquin J, Conti E. Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins. RNA (NEW YORK, N.Y.) 2017; 23:1028-1034. [PMID: 28389433 PMCID: PMC5473137 DOI: 10.1261/rna.061200.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 Å resolution crystal structure of a SMG8-SMG9 core complex from C. elegans We found that SMG8-SMG9 is a G-domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1. The SMG8-SMG9 heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans. Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. Fitting the GDP-bound SMG8-SMG9 structure in EM densities of the human SMG1-SMG8-SMG9 complex raises the possibility that the nucleotide site of SMG9 faces SMG1 and could impact the kinase conformation and/or regulation.
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Affiliation(s)
- Liang Li
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Jérome Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
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127
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Park OH, Park J, Yu M, An HT, Ko J, Kim YK. Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay. Genes Dev 2017; 30:2093-2105. [PMID: 27798850 PMCID: PMC5066615 DOI: 10.1101/gad.286484.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022]
Abstract
In this study, Park et al. investigated the molecular mechanisms regulating glucocorticoid receptor-mediated mRNA decay (GMD). The authors characterize the molecular details of GMD, identify specific factors required for efficient GMD, and perform RNA sequencing, identifying many endogenous GMD substrates. Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complex-independent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.
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Affiliation(s)
- Ok Hyun Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Mira Yu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyoung-Tae An
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jesang Ko
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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128
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Valkov E, Jonas S, Weichenrieder O. Mille viae in eukaryotic mRNA decapping. Curr Opin Struct Biol 2017; 47:40-51. [PMID: 28591671 DOI: 10.1016/j.sbi.2017.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2. Together with structure-based insight into decapping network assembly, we propose that DCP2-mediated decapping follows more than one path.
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Affiliation(s)
- Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zürich, Otto-Stern Weg 3, 8093 Zürich, Switzerland.
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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129
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Nickless A, Bailis JM, You Z. Control of gene expression through the nonsense-mediated RNA decay pathway. Cell Biosci 2017; 7:26. [PMID: 28533900 PMCID: PMC5437625 DOI: 10.1186/s13578-017-0153-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/12/2017] [Indexed: 11/25/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) was originally discovered as a cellular surveillance pathway that safeguards the quality of mRNA transcripts in eukaryotic cells. In its canonical function, NMD prevents translation of mutant mRNAs harboring premature termination codons (PTCs) by targeting them for degradation. However, recent studies have shown that NMD has a much broader role in gene expression by regulating the stability of many normal transcripts. In this review, we discuss the function of NMD in normal physiological processes, its dynamic regulation by developmental and environmental cues, and its association with human disease.
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Affiliation(s)
- Andrew Nickless
- Department of Cell Biology & Physiology, Washington University School of Medicine, Campus Box 8228, 660 S. Euclid Ave., St. Louis, MO 63110 USA
| | - Julie M Bailis
- Department of Oncology Research, Amgen, South San Francisco, CA 94080 USA
| | - Zhongsheng You
- Department of Cell Biology & Physiology, Washington University School of Medicine, Campus Box 8228, 660 S. Euclid Ave., St. Louis, MO 63110 USA
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130
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Harada N, Okuyama M, Yoshikatsu A, Yamamoto H, Ishiwata S, Hamada C, Hirose T, Shono M, Kuroda M, Tsutsumi R, Takeo J, Taketani Y, Nakaya Y, Sakaue H. Endoplasmic Reticulum Stress in Mice Increases Hepatic Expression of Genes Carrying a Premature Termination Codon via a Nutritional Status‐Independent GRP78‐Dependent Mechanism. J Cell Biochem 2017; 118:3810-3824. [DOI: 10.1002/jcb.26031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/04/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Nagakatsu Harada
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Maiko Okuyama
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Aya Yoshikatsu
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Hironori Yamamoto
- Faculty of Human LifeDepartment of Health and NutritionJin‐ai University3‐1‐1 Ohde‐choEchizen City915‐8586Japan
| | - Saori Ishiwata
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Chikako Hamada
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Tomoyo Hirose
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Masayuki Shono
- Support Center for Advanced Medical SciencesInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Masashi Kuroda
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Rie Tsutsumi
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Jiro Takeo
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
- Central Research LaboratoryNippon Suisan Kaisha32‐3 Nanakuni 1 ChomeHachiojiTokyo192‐0991Japan
| | - Yutaka Taketani
- Department of Clinical Nutrition and Food ManagementInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Yutaka Nakaya
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
| | - Hiroshi Sakaue
- Department of Nutrition and MetabolismInstitute of Biomedical SciencesTokushima University Graduate School3‐18‐15, Kuramoto‐choTokushima City770‐8503Japan
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131
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Iribarne M, Nishiwaki Y, Nakamura S, Araragi M, Oguri E, Masai I. Aipl1 is required for cone photoreceptor function and survival through the stability of Pde6c and Gc3 in zebrafish. Sci Rep 2017; 7:45962. [PMID: 28378769 PMCID: PMC5381001 DOI: 10.1038/srep45962] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/07/2017] [Indexed: 12/18/2022] Open
Abstract
Genetic mutations in aryl hydrocarbon receptor interacting protein-like 1 (AIPL1) cause photoreceptor degeneration associated with Leber congenital amaurosis 4 (LCA4) in human patients. Here we report retinal phenotypes of a zebrafish aipl1 mutant, gold rush (gosh). In zebrafish, there are two aipl1 genes, aipl1a and aipl1b, which are expressed mainly in rods and cones, respectively. The gosh mutant gene encodes cone-specific aipl1, aipl1b. Cone photoreceptors undergo progressive degeneration in the gosh mutant, indicating that aipl1b is required for cone survival. Furthermore, the cone-specific subunit of cGMP phosphodiesterase 6 (Pde6c) is markedly decreased in the gosh mutant, and the gosh mutation genetically interacts with zebrafish pde6c mutation eclipse (els). These data suggest that Aipl1 is required for Pde6c stability and function. In addition to Pde6c, we found that zebrafish cone-specific guanylate cyclase, zGc3, is also decreased in the gosh and els mutants. Furthermore, zGc3 knockdown embryos showed a marked reduction in Pde6c. These observations illustrate the interdependence of cGMP metabolism regulators between Aipl1, Pde6c, and Gc3 in photoreceptors.
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Affiliation(s)
- Maria Iribarne
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Yuko Nishiwaki
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Shohei Nakamura
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Masato Araragi
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Eri Oguri
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Ichiro Masai
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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132
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Colombo M, Karousis ED, Bourquin J, Bruggmann R, Mühlemann O. Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways. RNA (NEW YORK, N.Y.) 2017; 23:189-201. [PMID: 27864472 PMCID: PMC5238794 DOI: 10.1261/rna.059055.116] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/05/2016] [Indexed: 05/02/2023]
Abstract
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors. Our data revealed that SMG6 and SMG7 act on essentially the same transcripts, indicating extensive redundancy between the endo- and exonucleolytic decay routes. Besides mRNAs, we also identified as NMD targets many long noncoding RNAs as well as miRNA and snoRNA host genes. The NMD target feature with the most predictive value is an intron in the 3' UTR, followed by the presence of upstream open reading frames (uORFs) and long 3' UTRs. Furthermore, the 3' UTRs of NMD-targeted transcripts tend to have an increased GC content and to be phylogenetically less conserved when compared to 3' UTRs of NMD insensitive transcripts.
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Affiliation(s)
- Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, CH-3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Joël Bourquin
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, CH-3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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133
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Kejiou NS, Palazzo AF. mRNA localization as a rheostat to regulate subcellular gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [DOI: 10.1002/wrna.1416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Nevraj S. Kejiou
- Department of Biochemistry; University of Toronto; Toronto Canada
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134
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Balistreri G, Bognanni C, Mühlemann O. Virus Escape and Manipulation of Cellular Nonsense-Mediated mRNA Decay. Viruses 2017; 9:v9010024. [PMID: 28124995 PMCID: PMC5294993 DOI: 10.3390/v9010024] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/05/2017] [Accepted: 01/13/2017] [Indexed: 12/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD), a cellular RNA turnover pathway targeting RNAs with features resulting in aberrant translation termination, has recently been found to restrict the replication of positive-stranded RNA ((+)RNA) viruses. As for every other antiviral immune system, there is also evidence of viruses interfering with and modulating NMD to their own advantage. This review will discuss our current understanding of why and how NMD targets viral RNAs, and elaborate counter-defense strategies viruses utilize to escape NMD.
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Affiliation(s)
- Giuseppe Balistreri
- Department of Biosciences, University of Helsinki, Helsinki FIN-00014, Finland.
| | - Claudia Bognanni
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland.
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland.
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135
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Matos ML, Lapyckyj L, Rosso M, Besso MJ, Mencucci MV, Briggiler CIM, Giustina S, Furlong LI, Vazquez-Levin MH. Identification of a Novel Human E-Cadherin Splice Variant and Assessment of Its Effects Upon EMT-Related Events. J Cell Physiol 2016; 232:1368-1386. [PMID: 27682981 DOI: 10.1002/jcp.25622] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022]
Abstract
Epithelial Cadherin (E-cadherin) is involved in calcium-dependent cell-cell adhesion and signal transduction. The E-cadherin decrease/loss is a hallmark of Epithelial to Mesenchymal Transition (EMT), a key event in tumor progression. The underlying molecular mechanisms that trigger E-cadherin loss and consequent EMT have not been completely elucidated. This study reports the identification of a novel human E-cadherin variant mRNA produced by alternative splicing. A bioinformatics evaluation of the novel mRNA sequence and biochemical verifications suggest its regulation by Nonsense-Mediated mRNA Decay (NMD). The novel E-cadherin variant was detected in 29/42 (69%) human tumor cell lines, expressed at variable levels (E-cadherin variant expression relative to the wild type mRNA = 0.05-11.6%). Stable transfection of the novel E-cadherin variant in MCF-7 cells (MCF7Ecadvar) resulted in downregulation of wild type E-cadherin expression (transcript/protein) and EMT-related changes, among them acquisition of a fibroblastic-like cell phenotype, increased expression of Twist, Snail, Zeb1, and Slug transcriptional repressors and decreased expression of ESRP1 and ESRP2 RNA binding proteins. Moreover, loss of cytokeratins and gain of vimentin, N-cadherin and Dysadherin/FXYD5 proteins was observed. Dramatic changes in cell behavior were found in MCF7Ecadvar, as judged by the decreased cell-cell adhesion (Hanging-drop assay), increased cell motility (Wound Healing) and increased cell migration (Transwell) and invasion (Transwell w/Matrigel). Some changes were found in MCF-7 cells incubated with culture medium supplemented with conditioned medium from HEK-293 cells transfected with the E-cadherin variant mRNA. Further characterization of the novel E-cadherin variant will help understanding the molecular basis of tumor progression and improve cancer diagnosis. J. Cell. Physiol. 232: 1368-1386, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- María Laura Matos
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - Lara Lapyckyj
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - Marina Rosso
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - María José Besso
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - María Victoria Mencucci
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - Clara Isabel Marín Briggiler
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - Silvina Giustina
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - Laura Inés Furlong
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
| | - Mónica Hebe Vazquez-Levin
- Instituto de Biología y Medicina Experimental (IBYME). National Research Council of Argentina (CONICET). Fundación IBYME, Vuelta de Obligado 2490, Buenos Aires, Argentina
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136
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Woodward LA, Mabin JW, Gangras P, Singh G. The exon junction complex: a lifelong guardian of mRNA fate. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 28008720 DOI: 10.1002/wrna.1411] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 12/28/2022]
Abstract
During messenger RNA (mRNA) biogenesis and processing in the nucleus, many proteins are imprinted on mRNAs assembling them into messenger ribonucleoproteins (mRNPs). Some of these proteins remain stably bound within mRNPs and have a long-lasting impact on their fate. One of the best-studied examples is the exon junction complex (EJC), a multiprotein complex deposited primarily 24 nucleotides upstream of exon-exon junctions as a consequence of pre-mRNA splicing. The EJC maintains a stable, sequence-independent, hold on the mRNA until its removal during translation in the cytoplasm. Acting as a molecular shepherd, the EJC travels with mRNA across the cellular landscape coupling pre-mRNA splicing to downstream, posttranscriptional processes such as mRNA export, mRNA localization, translation, and nonsense-mediated mRNA decay (NMD). In this review, we discuss our current understanding of the EJC's functions during these processes, and expound its newly discovered functions (e.g., pre-mRNA splicing). Another focal point is the recently unveiled in vivo EJC interactome, which has shed new light on the EJC's location on the spliced RNAs and its intimate relationship with other mRNP components. We summarize new strides being made in connecting the EJC's molecular function with phenotypes, informed by studies of human disorders and model organisms. The progress toward understanding EJC functions has revealed, in its wake, even more questions, which are discussed throughout. WIREs RNA 2017, 8:e1411. doi: 10.1002/wrna.1411 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Lauren A Woodward
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Justin W Mabin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Pooja Gangras
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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137
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Abstract
NMD is a highly conserved pathway that degrades specific subsets of RNAs. There is increasing evidence for roles of NMD in development. In this commentary, we focus on spermatogenesis, a process dramatically impeded upon loss or disruption of NMD. NMD requires strict regulation for normal spermatogenesis, as loss of a newly discovered NMD repressor, UPF3A, also causes spermatogenic defects, most prominently during meiosis. We discuss the unusual evolution of UPF3A, whose paralog, UPF3B, has the opposite biochemical function and acts in brain development. We also discuss the regulation of NMD during germ cell development, including in chromatoid bodies, which are specifically found in haploid germ cells. The ability of NMD to coordinately degrade batteries of RNAs in a regulated fashion during development is akin to the action of transcriptional pathways, yet has the advantage of driving rapid changes in gene expression.
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Affiliation(s)
- Samantha H Jones
- a Department of Reproductive Medicine , School of Medicine, University of California, San Diego , La Jolla , CA , USA
| | - Miles Wilkinson
- a Department of Reproductive Medicine , School of Medicine, University of California, San Diego , La Jolla , CA , USA.,b Institute of Genomic Medicine, University of California , San Diego, La Jolla , CA , USA
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138
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Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries. Viruses 2016; 8:v8110320. [PMID: 27886048 PMCID: PMC5127034 DOI: 10.3390/v8110320] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
The human immunodeficiency virus type-1 (HIV-1) unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs) containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1), Staufen double-stranded RNA binding protein 1/2 (STAU1/2), or components of miRNA-induced silencing complex (miRISC) and processing bodies (PBs). More recently, the HIV-1 unspliced mRNA was shown to contain N⁶-methyladenosine (m⁶A), allowing the recruitment of YTH N⁶-methyladenosine RNA binding protein 2 (YTHDF2), an m⁶A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.
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Abstract
Eukaryotic gene expression is extensively controlled at the level of mRNA stability and the mechanisms underlying this regulation are markedly different from their archaeal and bacterial counterparts. We propose that two such mechanisms, nonsense‐mediated decay (NMD) and motif‐specific transcript destabilization by CCCH‐type zinc finger RNA‐binding proteins, originated as a part of cellular defense against RNA pathogens. These branches of the mRNA turnover pathway might have been used by primeval eukaryotes alongside RNA interference to distinguish their own messages from those of RNA viruses and retrotransposable elements. We further hypothesize that the subsequent advent of “professional” innate and adaptive immunity systems allowed NMD and the motif‐triggered mechanisms to be efficiently repurposed for regulation of endogenous cellular transcripts. This scenario explains the rapid emergence of archetypical mRNA destabilization pathways in eukaryotes and argues that other aspects of post‐transcriptional gene regulation in this lineage might have been derived through a similar exaptation route.
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Affiliation(s)
- Fursham M Hamid
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Eugene V Makeyev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Centre for Developmental Neurobiology, King's College London, London, UK
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