1
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Boo SH, Shin MK, Ha H, Woo JS, Kim YK. Transcriptome-wide analysis for glucocorticoid receptor-mediated mRNA decay reveals various classes of target transcripts. Mol Cells 2024:100130. [PMID: 39426683 DOI: 10.1016/j.mocell.2024.100130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 10/09/2024] [Accepted: 10/14/2024] [Indexed: 10/21/2024] Open
Abstract
The glucocorticoid receptor (GR) can bind to DNA or RNA, eliciting transcriptional activation/repression or rapid mRNA degradation, respectively. Although GR-mediated transcriptional regulation has been well-characterized, the molecular details of rapid mRNA degradation induced by glucocorticoids (GCs) are not yet fully understood. Here, we demonstrate that GC-induced GR-mediated mRNA decay (GMD) takes place in the nucleus and the cytoplasm, acting on pre-mRNAs and mRNAs. We also performed cross-linking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) analysis for GMD factors (GR, YBX1, and HRSP12) and mRNA sequencing (mRNA-seq) analysis to identify endogenous GMD substrates. Our comprehensive CLIP-seq and mRNA sequencing analyses reveal that a range of cellular transcripts containing a common binding site for GR, YBX1, and HRSP12 are preferential targets for GMD, suggesting possible new functions of GMD in various biological events.
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Affiliation(s)
- Sung Ho Boo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyung Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
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2
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Oh RY, AlMail A, Cheerie D, Guirguis G, Hou H, Yuki KE, Haque B, Thiruvahindrapuram B, Marshall CR, Mendoza-Londono R, Shlien A, Kyriakopoulou LG, Walker S, Dowling JJ, Wilson MD, Costain G. A systematic assessment of the impact of rare canonical splice site variants on splicing using functional and in silico methods. HGG ADVANCES 2024; 5:100299. [PMID: 38659227 PMCID: PMC11144818 DOI: 10.1016/j.xhgg.2024.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
Canonical splice site variants (CSSVs) are often presumed to cause loss-of-function (LoF) and are assigned very strong evidence of pathogenicity (according to American College of Medical Genetics/Association for Molecular Pathology criterion PVS1). The exact nature and predictability of splicing effects of unselected rare CSSVs in blood-expressed genes are poorly understood. We identified 168 rare CSSVs in blood-expressed genes in 112 individuals using genome sequencing, and studied their impact on splicing using RNA sequencing (RNA-seq). There was no evidence of a frameshift, nor of reduced expression consistent with nonsense-mediated decay, for 25.6% of CSSVs: 17.9% had wildtype splicing only and normal junction depths, 3.6% resulted in cryptic splice site usage and in-frame insertions or deletions, 3.6% resulted in full exon skipping (in frame), and 0.6% resulted in full intron inclusion (in frame). Blind to these RNA-seq data, we attempted to predict the precise impact of CSSVs by applying in silico tools and the ClinGen Sequence Variant Interpretation Working Group 2018 guidelines for applying PVS1 criterion. The predicted impact on splicing using (1) SpliceAI, (2) MaxEntScan, and (3) AutoPVS1, an automatic classification tool for PVS1 interpretation of null variants that utilizes Ensembl Variant Effect Predictor and MaxEntScan, was concordant with RNA-seq analyses for 65%, 63%, and 61% of CSSVs, respectively. In summary, approximately one in four rare CSSVs did not show evidence for LoF based on analysis of RNA-seq data. Predictions from in silico methods were often discordant with findings from RNA-seq. More caution may be warranted in applying PVS1-level evidence to CSSVs in the absence of functional data.
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Affiliation(s)
- Rachel Y Oh
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ali AlMail
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - David Cheerie
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - George Guirguis
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Huayun Hou
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Kyoko E Yuki
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada
| | - Bushra Haque
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Christian R Marshall
- Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lianna G Kyriakopoulou
- Division of Genome Diagnostics, Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Susan Walker
- The Centre for Applied Genomics, SickKids Research Institute, Toronto, ON, Canada
| | - James J Dowling
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada; Division of Neurology, Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada.
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3
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Jiang H, Zhang Y, Hu J, Wang Z, Li G, Lu Y. An alternative spliced UPF2 transcript in pancreatic inflammatory myofibroblastic tumors. Biochem Biophys Res Commun 2024; 691:149306. [PMID: 38056247 DOI: 10.1016/j.bbrc.2023.149306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Inflammatory myofibroblastic tumors (IMTs) are characterized by myofibroblast proliferation and an inflammatory cell infiltrate. Our previous study on IMTs reveals that disrupt NMD pathway causes to lower the threshold for triggering the immune cell infiltration, thereby resulting in inappropriate immune activation. However, myofibroblast differentiation and proliferation is not yet known. METHODS RT-PCR, RT-qPCR, DNA sequence, western bolt, 5'race analysis and site-specific mutagenesis were used in this study. RESULTS Here, an alternative spliced (ALS) UPF2 mRNA skipping exon 2 and 3 and corresponding to the truncated UPF2 protein were found in 2 pancreatic IMTs. We showed that the uORF present in the 5'UTR of UPF2 mRNA is responsible for the translation inhibition, whiles ALS UPF2 is more facilitated to be translated into the truncated UPF2 protein. Several mRNA targets of the NMD were upregulated in IMT samples, indicating that the truncated UPF2 function is strongly perturbed, resulted in disrupted NMD pathway in IMTs. These upregulated NMD targets included cdkn1a expression and the generation of high levels of p21 (waf1/cip1), which may contribute to triggering IMTs. CONCLUSION The disrupt UPFs/NMD pathway may link to molecular alteration associated with differentiation and proliferation for IMTs.
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Affiliation(s)
- Hui Jiang
- Department of Pathology, First Affiliated Hospital, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Yunshuo Zhang
- Department of Pathology, First Affiliated Hospital, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Jiayang Hu
- Department of Hepatopancreatobiliary Surgery, First Affiliated Hospital, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Zhen Wang
- Department of Hepatopancreatobiliary Surgery, First Affiliated Hospital, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Gang Li
- Department of Hepatopancreatobiliary Surgery, First Affiliated Hospital, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
| | - Yanjun Lu
- Department of Hepatopancreatobiliary Surgery, First Affiliated Hospital, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
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4
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Ottens F, Efstathiou S, Hoppe T. Cutting through the stress: RNA decay pathways at the endoplasmic reticulum. Trends Cell Biol 2023:S0962-8924(23)00236-2. [PMID: 38008608 DOI: 10.1016/j.tcb.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
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Affiliation(s)
- Franziska Ottens
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sotirios Efstathiou
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
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5
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
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6
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Chousal JN, Sohni A, Vitting-Seerup K, Cho K, Kim M, Tan K, Porse B, Wilkinson MF, Cook-Andersen H. Progression of the pluripotent epiblast depends upon the NMD factor UPF2. Development 2022; 149:dev200764. [PMID: 36255229 PMCID: PMC9687065 DOI: 10.1242/dev.200764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that degrades RNAs harboring in-frame stop codons in specific contexts. Loss of NMD factors leads to embryonic lethality in organisms spanning the phylogenetic scale, but the mechanism remains unknown. Here, we report that the core NMD factor, UPF2, is required for expansion of epiblast cells within the inner cell mass of mice in vivo. We identify NMD target mRNAs in mouse blastocysts - both canonical and alternatively processed mRNAs - including those encoding cell cycle arrest and apoptosis factors, raising the possibility that NMD is essential for embryonic cell proliferation and survival. In support, the inner cell mass of Upf2-null blastocysts rapidly regresses with outgrowth and is incompetent for embryonic stem cell derivation in vitro. In addition, we uncovered concordant temporal- and lineage-specific regulation of NMD factors and mRNA targets, indicative of a shift in NMD magnitude during peri-implantation development. Together, our results reveal developmental and molecular functions of the NMD pathway in the early embryo.
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Affiliation(s)
- Jennifer N. Chousal
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
- Section for Bioinformatics, Health Technology, Technical University of Denmark (DTU), 2800 Kongens Lyngby, Denmark
| | - Kyucheol Cho
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Kim
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kun Tan
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Liu M, Kang GJ, Dudley SC. Preventing unfolded protein response-induced ion channel dysregulation to treat arrhythmias. Trends Mol Med 2022; 28:443-451. [DOI: 10.1016/j.molmed.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 01/15/2023]
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8
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De S, Edwards DM, Dwivedi V, Wang J, Varsally W, Dixon HL, Singh AK, Owuamalam PO, Wright MT, Summers RP, Hossain MN, Price EM, Wojewodzic MW, Falciani F, Hodges NJ, Saponaro M, Tanaka K, Azzalin CM, Baumann P, Hebenstreit D, Brogna S. Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe. Nucleic Acids Res 2021; 50:350-367. [PMID: 34928380 PMCID: PMC8754637 DOI: 10.1093/nar/gkab1249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript, Upf1 might influence Pol II phosphorylation and transcription.
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Affiliation(s)
- Sandip De
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Division of Cellular and Gene Therapies, Tumor Vaccines and Biotechnology Branch, Center for Biologics and Evaluation Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David M Edwards
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Vibha Dwivedi
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Jianming Wang
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Wazeer Varsally
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Hannah L Dixon
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Anand K Singh
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Interdisciplinary School of Life Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Precious O Owuamalam
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Matthew T Wright
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Reece P Summers
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Md Nazmul Hossain
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Department of Microbial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Emily M Price
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Marcin W Wojewodzic
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Department of Environmental Health, Norwegian Institute of Public Health, Oslo, Norway & Department of Research, Cancer Registry of Norway, Oslo University Hospital, Oslo, Norway & Environmental Genomics, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Francesco Falciani
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Nikolas J Hodges
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, UK
| | - Kayoko Tanaka
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes (iMM), Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | | | | | - Saverio Brogna
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
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9
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Ghiasi SM, Rutter GA. Consequences for Pancreatic β-Cell Identity and Function of Unregulated Transcript Processing. Front Endocrinol (Lausanne) 2021; 12:625235. [PMID: 33763030 PMCID: PMC7984428 DOI: 10.3389/fendo.2021.625235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/26/2021] [Indexed: 12/25/2022] Open
Abstract
Mounting evidence suggests a role for alternative splicing (AS) of transcripts in the normal physiology and pathophysiology of the pancreatic β-cell. In the apparent absence of RNA repair systems, RNA decay pathways are likely to play an important role in controlling the stability, distribution and diversity of transcript isoforms in these cells. Around 35% of alternatively spliced transcripts in human cells contain premature termination codons (PTCs) and are targeted for degradation via nonsense-mediated decay (NMD), a vital quality control process. Inflammatory cytokines, whose levels are increased in both type 1 (T1D) and type 2 (T2D) diabetes, stimulate alternative splicing events and the expression of NMD components, and may or may not be associated with the activation of the NMD pathway. It is, however, now possible to infer that NMD plays a crucial role in regulating transcript processing in normal and stress conditions in pancreatic β-cells. In this review, we describe the possible role of Regulated Unproductive Splicing and Translation (RUST), a molecular mechanism embracing NMD activity in relationship to AS and translation of damaged transcript isoforms in these cells. This process substantially reduces the abundance of non-functional transcript isoforms, and its dysregulation may be involved in pancreatic β-cell failure in diabetes.
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Affiliation(s)
- Seyed M. Ghiasi
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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Zhu Y, Ren C, Yang L. Effect of eukaryotic translation initiation factor 4A3 in malignant tumors. Oncol Lett 2021; 21:358. [PMID: 33747215 PMCID: PMC7967930 DOI: 10.3892/ol.2021.12619] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/19/2021] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic translation initiation factor 4A3 (EIF4A3), a key component of the exon junction complex, is widely involved in RNA splicing and nonsense-mediated mRNA decay. EIF4A3 has also been reported to be involved in cell cycle regulation and apoptosis. Thus, EIF4A3 may serve as a pivotal regulatory factor involved in the occurrence and development of multiple diseases. Previous studies have demonstrated that EIF4A3 is mutated in neuromuscular degenerative lesions and is differentially expressed in several tumors, serving as a non-coding RNA binding protein to regulate its expression. In addition, studies have reported that inhibiting EIF4A3 can prevent tumor cell proliferation, thus, several researchers are trying to design and synthesize potent and selective EIF4A3 inhibitors. The present review summarizes the function of EIF4A3 in cell cycle and discusses it underlying molecular mechanisms that contribute to the occurrence of malignant diseases. In addition, EIF4A3 selective inhibitors, and bioinformatics analyses performed to analyze the expression and mutations of EIF4A3 in gynecological tumors and breast cancer, are also discussed.
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Affiliation(s)
- Yuanhang Zhu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Chenchen Ren
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Li Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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11
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Abstract
Long non-coding RNAs (LncRNAs) can bind to other proteins or RNAs to regulate gene expression, and its role in tumors has been extensively studied. A common RNA binding protein, UPF1, is also a key factor in a variety of RNA decay pathways. RNA decay pathways serve to control levels of particular RNA molecules. The expression of UPF1 is often dysregulated in tumors, an observation which suggests that UPF1 contributes to development of a variety of tumors. Herein, we review evidence from studies of fourteen lncRNAs interact with UPF1. The interaction between lncRNA and UPFI provide fundamental basis for cell transformation and tumorigenic growth.
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Affiliation(s)
- Junjian He
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Xiaoxin Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
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12
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Berland S, Haukanes BI, Juliusson PB, Houge G. Deep exploration of a CDKN1C mutation causing a mixture of Beckwith-Wiedemann and IMAGe syndromes revealed a novel transcript associated with developmental delay. J Med Genet 2020; 59:155-164. [PMID: 33443097 PMCID: PMC8788247 DOI: 10.1136/jmedgenet-2020-107401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/20/2020] [Accepted: 11/28/2020] [Indexed: 11/24/2022]
Abstract
Background Loss-of-function mutations in CDKN1C cause overgrowth, that is, Beckwith-Wiedemann syndrome (BWS), while gain-of-function variants in the gene’s PCNA binding motif cause a growth-restricted condition called IMAGe syndrome. We report on a boy with a remarkable mixture of both syndromes, with developmental delay and microcephaly as additional features. Methods Whole-exome DNA sequencing and ultra-deep RNA sequencing of leucocyte-derived and fibroblast-derived mRNA were performed in the family. Results We found a maternally inherited variant in the IMAGe hotspot region: NM_000076.2(CDKN1C) c.822_826delinsGAGCTG. The asymptomatic mother had inherited this variant from her mosaic father with mild BWS features. This delins caused tissue-specific frameshifting resulting in at least three novel mRNA transcripts in the boy. First, a splice product causing CDKN1C truncation was the likely cause of BWS. Second, an alternative splice product in fibroblasts encoded IMAGe-associated amino acid substitutions. Third, we speculate that developmental delay is caused by a change in the alternative CDKN1C-201 (ENST00000380725.1) transcript, encoding a novel isoform we call D (UniProtKB: A6NK88). Isoform D is distinguished from isoforms A and B by alternative splicing within exon 1 that changes the reading frame of the last coding exon. Remarkably, this delins changed the reading frame back to the isoform A/B type, resulting in a hybrid D–A/B isoform. Conclusion Three different cell-type-dependent RNA products can explain the co-occurrence of both BWS and IMAGe features in the boy. Possibly, brain expression of hybrid isoform D–A/B is the cause of developmental delay and microcephaly, a phenotypic feature not previously reported in CDKN1C patients.
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Affiliation(s)
- Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Petur Benedikt Juliusson
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Department of Paediatrics, Haukeland University Hospital, Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
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13
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Correa-Vela M, Lupo V, Montpeyó M, Sancho P, Marcé-Grau A, Hernández-Vara J, Darling A, Jenkins A, Fernández-Rodríguez S, Tello C, Ramírez-Jiménez L, Pérez B, Sánchez-Montáñez Á, Macaya A, Sobrido MJ, Martinez-Vicente M, Pérez-Dueñas B, Espinós C. Impaired proteasome activity and neurodegeneration with brain iron accumulation in FBXO7 defect. Ann Clin Transl Neurol 2020; 7:1436-1442. [PMID: 32767480 PMCID: PMC7448169 DOI: 10.1002/acn3.51095] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 12/21/2022] Open
Abstract
FBXO7 is implicated in the ubiquitin-proteasome system and parkin-mediated mitophagy. FBXO7defects cause a levodopa-responsive parkinsonian-pyramidal syndrome(PPS). METHODS We investigated the disease molecular bases in a child with PPS and brain iron accumulation. RESULTS A novel homozygous c.368C>G (p.S123*) FBXO7 mutation was identified in a child with spastic paraplegia, epilepsy, cerebellar degeneration, levodopa nonresponsive parkinsonism, and brain iron deposition. Patient's fibroblasts assays demonstrated an absence of FBXO7 RNA expression leading to impaired proteasome degradation and accumulation of poly-ubiquitinated proteins. CONCLUSION This novel FBXO7 phenotype associated with impaired proteasome activity overlaps with neurodegeneration with brain iron accumulation disorders.
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Affiliation(s)
- Marta Correa-Vela
- Department of Pediatric Neurology, Hospital Universitari Vall d'Hebron, Vall d´Hebron Institut de Recerca, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Joint Units INCLIVA & IIS La Fe Rare Diseases, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Marta Montpeyó
- Neurodegenerative diseases-CIBERNED, Vall d´Hebron, Institut de Recerca, Barcelona, Spain
| | - Paula Sancho
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Joint Units INCLIVA & IIS La Fe Rare Diseases, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Anna Marcé-Grau
- Department of Pediatric Neurology, Hospital Universitari Vall d'Hebron, Vall d´Hebron Institut de Recerca, Barcelona, Spain
| | | | - Alejandra Darling
- Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Alison Jenkins
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Sandra Fernández-Rodríguez
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Cristina Tello
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Laura Ramírez-Jiménez
- Unit of Genomics and Traslational Genetics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Belén Pérez
- Department of Molecular Biology, Centro de Biología Molecular Severo-Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), CIBER on Rare Diseases (CIBERER), Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), Madrid, Spain
| | - Ángel Sánchez-Montáñez
- Department of Pediatric Radiology, Hospital Universitari Vall d'Hebrón, Barcelona, Spain
| | - Alfons Macaya
- Department of Pediatric Neurology, Hospital Universitari Vall d'Hebron, Vall d´Hebron Institut de Recerca, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María J Sobrido
- Neurogenetics Research Group, Instituto de Investigaciones Sanitarias (IDIS), Fundación Pública Galega de Medicina Xenómica, and CIBER on Rare Diseases (CIBERER), Santiago de Compostela, Spain
| | | | - Belén Pérez-Dueñas
- Department of Pediatric Neurology, Hospital Universitari Vall d'Hebron, Vall d´Hebron Institut de Recerca, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Espinós
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Joint Units INCLIVA & IIS La Fe Rare Diseases, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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14
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Müller-McNicoll M, Rossbach O, Hui J, Medenbach J. Auto-regulatory feedback by RNA-binding proteins. J Mol Cell Biol 2020; 11:930-939. [PMID: 31152582 PMCID: PMC6884704 DOI: 10.1093/jmcb/mjz043] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins (RBPs) are key regulators in post-transcriptional control of gene expression. Mutations that alter their activity or abundance have been implicated in numerous diseases such as neurodegenerative disorders and various types of cancer. This highlights the importance of RBP proteostasis and the necessity to tightly control the expression levels and activities of RBPs. In many cases, RBPs engage in an auto-regulatory feedback by directly binding to and influencing the fate of their own mRNAs, exerting control over their own expression. For this feedback control, RBPs employ a variety of mechanisms operating at all levels of post-transcriptional regulation of gene expression. Here we review RBP-mediated autogenous feedback regulation that either serves to maintain protein abundance within a physiological range (by negative feedback) or generates binary, genetic on/off switches important for e.g. cell fate decisions (by positive feedback).
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Affiliation(s)
- Michaela Müller-McNicoll
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Strasse 13, D-60438 Frankfurt am Main, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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15
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Powers KT, Szeto JYA, Schaffitzel C. New insights into no-go, non-stop and nonsense-mediated mRNA decay complexes. Curr Opin Struct Biol 2020; 65:110-118. [PMID: 32688260 DOI: 10.1016/j.sbi.2020.06.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 11/26/2022]
Abstract
Eukaryotes possess a variety of translational control mechanisms which function in the surveillance of mRNAs, discriminating between normal and aberrant translation elongation and termination, triggering mRNA decay. The three major evolutionarily conserved eukaryotic pathways are No-Go, Non-Stop and Nonsense-Mediated mRNA Decay. Recent findings suggest that stalling of the ribosome, due to mRNA secondary structure or translation into poly(A)-stretches, leads to ribosome collisions which are detected by No-Go/Non-Stop mRNA decay factors. Subsequent ribosome ubiquitination at the interface of two collided ribosomes is considered the signal for mRNA decay. Similarly, translation termination at a premature stop codon is slower than normal, leading to recruitment and activation of nonsense-mediated mRNA decay factors, including SMG1-8-9. Here, we detail new insights into the molecular mechanisms of these pathways.
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Affiliation(s)
- Kyle T Powers
- University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Jenn-Yeu Alvin Szeto
- University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Christiane Schaffitzel
- University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom.
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16
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Lavysh D, Neu-Yilik G. UPF1-Mediated RNA Decay-Danse Macabre in a Cloud. Biomolecules 2020; 10:E999. [PMID: 32635561 PMCID: PMC7407380 DOI: 10.3390/biom10070999] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is the prototype example of a whole family of RNA decay pathways that unfold around a common central effector protein called UPF1. While NMD in yeast appears to be a linear pathway, NMD in higher eukaryotes is a multifaceted phenomenon with high variability with respect to substrate RNAs, degradation efficiency, effector proteins and decay-triggering RNA features. Despite increasing knowledge of the mechanistic details, it seems ever more difficult to define NMD and to clearly distinguish it from a growing list of other UPF1-mediated RNA decay pathways (UMDs). With a focus on mammalian, we here critically examine the prevailing NMD models and the gaps and inconsistencies in these models. By exploring the minimal requirements for NMD and other UMDs, we try to elucidate whether they are separate and definable pathways, or rather variations of the same phenomenon. Finally, we suggest that the operating principle of the UPF1-mediated decay family could be considered similar to that of a computing cloud providing a flexible infrastructure with rapid elasticity and dynamic access according to specific user needs.
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Affiliation(s)
- Daria Lavysh
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany;
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
- Department Clinical Pediatric Oncology, Hopp Kindertumorzentrum am NCT Heidelberg, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany;
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
- Department Clinical Pediatric Oncology, Hopp Kindertumorzentrum am NCT Heidelberg, 69120 Heidelberg, Germany
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17
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Borden KLB, Volpon L. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. RNA Biol 2020; 17:1239-1251. [PMID: 32496897 PMCID: PMC7549709 DOI: 10.1080/15476286.2020.1766179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Translation initiation is a critical facet of gene expression with important impacts that underlie cellular responses to stresses and environmental cues. Its dysregulation in many diseases position this process as an important area for the development of new therapeutics. The gateway translation factor eIF4E is typically considered responsible for ‘global’ or ‘canonical’ m7G cap-dependent translation. However, eIF4E impacts translation of specific transcripts rather than the entire translatome. There are many alternative cap-dependent translation mechanisms that also contribute to the translation capacity of the cell. We review the diversity of these, juxtaposing more recently identified mechanisms with eIF4E-dependent modalities. We also explore the multiplicity of functions played by translation factors, both within and outside protein synthesis, and discuss how these differentially contribute to their ultimate physiological impacts. For comparison, we discuss some modalities for cap-independent translation. In all, this review highlights the diverse mechanisms that engage and control translation in eukaryotes.
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Affiliation(s)
- Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
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18
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Sharma J, Keeling KM, Rowe SM. Pharmacological approaches for targeting cystic fibrosis nonsense mutations. Eur J Med Chem 2020; 200:112436. [PMID: 32512483 DOI: 10.1016/j.ejmech.2020.112436] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022]
Abstract
Cystic fibrosis (CF) is a monogenic autosomal recessive disorder. The clinical manifestations of the disease are caused by ∼2,000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. It is unlikely that any one approach will be efficient in correcting all defects. The recent approvals of ivacaftor, lumacaftor/ivacaftor and elexacaftor/tezacaftor/ivacaftor represent the genesis of a new era of precision combination medicine for the CF patient population. In this review, we discuss targeted translational readthrough approaches as mono and combination therapies for CFTR nonsense mutations. We examine the current status of efficacy of translational readthrough/nonsense suppression therapies and their limitations, including non-native amino acid incorporation at PTCs and nonsense-mediated mRNA decay (NMD), along with approaches to tackle these limitations. We further elaborate on combining various therapies such as readthrough agents, NMD inhibitors, and corrector/potentiators to improve the efficacy and safety of suppression therapy. These mutation specific strategies that are directed towards the basic CF defects should positively impact CF patients bearing nonsense mutations.
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Affiliation(s)
- Jyoti Sharma
- Department of Medicine, University of Alabama at Birmingham (UAB), USA; Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), USA; Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), USA
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham (UAB), USA; Department of Pediatrics, University of Alabama at Birmingham (UAB), USA; Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), USA.
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19
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Lin Y, Liang R, Qiu Y, Lv Y, Zhang J, Qin G, Yuan C, Liu Z, Li Y, Zou D, Mao Y. Expression and gene regulation network of RBM8A in hepatocellular carcinoma based on data mining. Aging (Albany NY) 2020; 11:423-447. [PMID: 30670676 PMCID: PMC6366983 DOI: 10.18632/aging.101749] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/25/2018] [Indexed: 12/11/2022]
Abstract
RNA binding motif protein 8A (RBM8A) is an RNA binding protein in a core component of the exon junction complex. Abnormal RBM8A expression is associated with carcinogenesis. We used sequencing data from the Cancer Genome Atlas database and Gene Expression Omnibus, analyzed RBM8A expression and gene regulation networks in hepatocellular carcinoma (HCC). Expression was analyzed using OncomineTM and Gene Expression Profiling Interactive Analysis tools, while RBM8A alterations and related functional networks were identified using cBioPortal. LinkedOmics was used to identify differential gene expression with RBM8A and to analyze Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. Gene enrichment analysis examined target networks of kinases, miRNAs and transcription factors. We found that RBM8A is overexpressed and the RBM8A gene often amplified in HCC. Expression of this gene is linked to functional networks involving the ribosome and RNA metabolic signaling pathways. Functional network analysis suggested that RBM8A regulates the spliceosome, ribosome, DNA replication and cell cycle signaling via pathways involving several cancer-related kinases, miRNAs and E2F Transcription Factor 1. Our results demonstrate that data mining efficiently reveals information about RBM8A expression and potential regulatory networks in HCC, laying a foundation for further study of the role of RBM8A in carcinogenesis.
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Affiliation(s)
- Yan Lin
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Rong Liang
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yufen Qiu
- Maternal and Child Health Hospital and Obstetrics and Gynecology Hospital of Guangxi Zhuang Autonomous Region, Guangxi 530021, People's Republic of China
| | - Yufeng Lv
- Department of Medical Oncology, Affiliated Langdong Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Jinyan Zhang
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Gang Qin
- The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Chunling Yuan
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Zhihui Liu
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yongqiang Li
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Donghua Zou
- The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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20
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Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics. Cancers (Basel) 2020; 12:cancers12030765. [PMID: 32213869 PMCID: PMC7140085 DOI: 10.3390/cancers12030765] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a surveillance pathway used by cells to control the quality mRNAs and to fine-tune transcript abundance. NMD plays an important role in cell cycle regulation, cell viability, DNA damage response, while also serving as a barrier to virus infection. Disturbance of this control mechanism caused by genetic mutations or dys-regulation of the NMD pathway can lead to pathologies, including neurological disorders, immune diseases and cancers. The role of NMD in cancer development is complex, acting as both a promoter and a barrier to tumour progression. Cancer cells can exploit NMD for the downregulation of key tumour suppressor genes, or tumours adjust NMD activity to adapt to an aggressive immune microenvironment. The latter case might provide an avenue for therapeutic intervention as NMD inhibition has been shown to lead to the production of neoantigens that stimulate an immune system attack on tumours. For this reason, understanding the biology and co-option pathways of NMD is important for the development of novel therapeutic agents. Inhibitors, whose design can make use of the many structures available for NMD study, will play a crucial role in characterizing and providing diverse therapeutic options for this pathway in cancer and other diseases.
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21
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Screening Readthrough Compounds to Suppress Nonsense Mutations: Possible Application to β-Thalassemia. J Clin Med 2020; 9:jcm9020289. [PMID: 31972957 PMCID: PMC7073686 DOI: 10.3390/jcm9020289] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Several types of thalassemia (including β039-thalassemia) are caused by nonsense mutations in genes controlling globin production, leading to premature translation termination and mRNA destabilization mediated by the nonsense mediated mRNA decay. Drugs (for instance, aminoglycosides) can be designed to suppress premature translation termination by inducing readthrough (or nonsense suppression) at the premature termination codon. These findings have introduced new hopes for the development of a pharmacologic approach to cure this genetic disease. In the present review, we first summarize the principle and current status of the chemical relief for the expression of functional proteins from genes otherwise unfruitful for the presence of nonsense mutations. Second, we compare data available on readthrough molecules for β0-thalassemia. The examples reported in the review strongly suggest that ribosomal readthrough should be considered as a therapeutic approach for the treatment of β0-thalassemia caused by nonsense mutations. Concluding, the discovery of molecules, exhibiting the property of inducing β-globin, such as readthrough compounds, is of great interest and represents a hope for several patients, whose survival will depend on the possible use of drugs rendering blood transfusion and chelation therapy unnecessary.
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22
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Dyle MC, Kolakada D, Cortazar MA, Jagannathan S. How to get away with nonsense: Mechanisms and consequences of escape from nonsense-mediated RNA decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1560. [PMID: 31359616 PMCID: PMC10685860 DOI: 10.1002/wrna.1560] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/04/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is an evolutionarily conserved RNA quality control process that serves both as a mechanism to eliminate aberrant transcripts carrying premature stop codons, and to regulate expression of some normal transcripts. For a quality control process, NMD exhibits surprising variability in its efficiency across transcripts, cells, tissues, and individuals in both physiological and pathological contexts. Whether an aberrant RNA is spared or degraded, and by what mechanism, could determine the phenotypic outcome of a disease-causing mutation. Hence, understanding the variability in NMD is not only important for clinical interpretation of genetic variants but also may provide clues to identify novel therapeutic approaches to counter genetic disorders caused by nonsense mutations. Here, we discuss the current knowledge of NMD variability and the mechanisms that allow certain transcripts to escape NMD despite the presence of NMD-inducing features. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Michael C. Dyle
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Divya Kolakada
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A. Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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23
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Yeh JT, Hwang TC. Positional effects of premature termination codons on the biochemical and biophysical properties of CFTR. J Physiol 2019; 598:517-541. [PMID: 31585024 DOI: 10.1113/jp278418] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022] Open
Abstract
KEY POINTS Biochemical and biophysical characterizations of three nonsense mutations of cystic fibrosis transmembrane conductance regulator (CFTR) associated with a severe form of cystic fibrosis (CF) reveal the importance and heterogenous effects of the position of the premature termination codon (PTC) on the CFTR protein function. Electrophysiological studies of W1282X-CFTR, whose PTC is closer to the C-terminus of CFTR, suggest the presence of both C-terminus truncated CFTR proteins that are poorly functional and read-through, full-length products. For G542X- and E60X-CFTR, the only mechanism capable of generating functional proteins is the read-through, but the outcome of read-through products is highly variable depending on the interplay between the missense mutation caused by the read-through and the structural context of the protein. Pharmacological studies of these three PTCs with various CFTR modulators suggest position-dependent therapeutic strategies for these disease-inflicting mutations. ABSTRACT About one-third of genetic diseases and cancers are caused by the introduction of premature termination codons (PTCs). In theory, the location of the PTC in a gene determines the alternative mechanisms of translation, including premature cessation or reinitiation of translation, and read-through, resulting in differential effects on protein integrity. In this study, we used CFTR as a model system to investigate the positional effect of the PTC because of its well-understood structure-function relationship and pathophysiology. The characterization of three PTC mutations, E60X-, G542X- and W1282X-CFTR revealed heterogenous effects of these PTCs on CFTR function. The W1282X mutation results in both C-terminus truncated and read-through proteins that are partially or fully functional. In contrast, only the read-through protein is functional with E60X- and G542X-CFTR, although abundant N-terminus truncated proteins due to reinitiation of translation were detected in E60X-CFTR. Single-channel studies of the read-through proteins of E60X- and G542X-CFTR demonstrated that both mutations have a single-channel amplitude similar to wild type (WT), and good responses to high-affinity ATP analogues, suggesting intact ion permeation pathways and nucleotide binding domains (NBDs), albeit with reduced open probability (Po ). The comparison of the Po of these mutations with the proposed missense mutations revealed potential identities of the read-through products. Importantly, a majority of the functional protein studied responds to CFTR modulators like GLPG1837 and Lumacaftor. These results not only expand current understanding of the molecular (patho)physiology of CFTR, but also infer therapeutic strategies for different PTC mutations at large.
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Affiliation(s)
- Jiunn-Tyng Yeh
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tzyh-Chang Hwang
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Pharmacology and Physiology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
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24
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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25
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Abstract
Biomarker-driven personalized cancer therapy is a field of growing interest, and several molecular tests have been developed to detect biomarkers that predict, e.g., response of cancers to particular therapies. Identification of these molecules and understanding their molecular mechanisms is important for cancer prognosis and the development of therapeutics for late stage diseases. In the past, significant efforts have been placed on the discovery of protein or DNA-based biomarkers while only recently the class of long non-coding RNA (lncRNA) has emerged as a new category of biomarker. The mammalian genome is pervasively transcribed yielding a vast amount of non-protein-coding RNAs including lncRNAs. Hence, these transcripts represent a rich source of information that has the potential to significantly contribute to precision medicine in the future. Importantly, many lncRNAs are differentially expressed in carcinomas and they are emerging as potent regulators of tumor progression and metastasis. Here, we will highlight prime examples of lncRNAs that serve as marker for cancer progression or therapy response and which might represent promising therapeutic targets. Furthermore, we will introduce lncRNA targeting tools and strategies, and we will discuss potential pitfalls in translating these into clinical trials.
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26
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Singh AK, Choudhury SR, De S, Zhang J, Kissane S, Dwivedi V, Ramanathan P, Petric M, Orsini L, Hebenstreit D, Brogna S. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. eLife 2019; 8:e41444. [PMID: 30907728 PMCID: PMC6447362 DOI: 10.7554/elife.41444] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
UPF1 is an RNA helicase that is required for nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3'UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm by a mechanism that requires its RNA helicase activity. UPF1 is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary glands and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNAs, and cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and their export from the nucleus.
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Affiliation(s)
- Anand K Singh
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Sandip De
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Jie Zhang
- Life SciencesUniversity of WarwickCoventryUnited Kingdom
| | - Stephen Kissane
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Vibha Dwivedi
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Marija Petric
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Luisa Orsini
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Saverio Brogna
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
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27
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Rao S, Amorim R, Niu M, Breton Y, Tremblay MJ, Mouland AJ. Host mRNA decay proteins influence HIV-1 replication and viral gene expression in primary monocyte-derived macrophages. Retrovirology 2019; 16:3. [PMID: 30732620 PMCID: PMC6367771 DOI: 10.1186/s12977-019-0465-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/29/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mammalian cells harbour RNA quality control and degradative machineries such as nonsense-mediated mRNA decay that target cellular mRNAs for clearance from the cell to avoid aberrant gene expression. The role of the host mRNA decay pathways in macrophages in the context of human immunodeficiency virus type 1 (HIV-1) infection is yet to be elucidated. Macrophages are directly infected by HIV-1, mediate the dissemination of the virus and contribute to the chronic activation of the inflammatory response observed in infected individuals. Therefore, we characterized the effects of four host mRNA decay proteins, i.e., UPF1, UPF2, SMG6 and Staufen1, on viral replication in HIV-1-infected primary monocyte-derived macrophages (MDMs). RESULTS Steady-state expression levels of these host mRNA decay proteins were significantly downregulated in HIV-1-infected MDMs. Moreover, UPF2 and SMG6 inhibited HIV-1 gene expression in macrophages to a similar level achieved by SAMHD1, by directly influencing viral genomic RNA levels. Staufen1, a host protein also involved in UPF1-dependent mRNA decay and that acts at several HIV-1 replication steps, enhanced HIV-1 gene expression in MDMs. CONCLUSIONS These results provide new evidence for roles of host mRNA decay proteins in regulating HIV-1 replication in infected macrophages and can serve as potential targets for broad-spectrum antiviral therapeutics.
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Affiliation(s)
- Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Raquel Amorim
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada.,Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada
| | - Yann Breton
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Québec, Canada
| | - Michel J Tremblay
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, Québec, Canada.,Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Québec, Canada. .,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada. .,Department of Medicine, McGill University, Montréal, Québec, Canada.
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28
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Filatova EN, Utkin OV. The Role of Noncoding mRNA Isoforms in the Regulation of Gene Expression. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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29
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Huang L, Shum EY, Jones SH, Lou CH, Chousal J, Kim H, Roberts AJ, Jolly LA, Espinoza JL, Skarbrevik DM, Phan MH, Cook-Andersen H, Swerdlow NR, Gecz J, Wilkinson MF. A Upf3b-mutant mouse model with behavioral and neurogenesis defects. Mol Psychiatry 2018; 23:1773-1786. [PMID: 28948974 PMCID: PMC5869067 DOI: 10.1038/mp.2017.173] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/05/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA degradation pathway that acts on RNAs terminating their reading frames in specific contexts. NMD is regulated in a tissue-specific and developmentally controlled manner, raising the possibility that it influences developmental events. Indeed, loss or depletion of NMD factors have been shown to disrupt developmental events in organisms spanning the phylogenetic scale. In humans, mutations in the NMD factor gene, UPF3B, cause intellectual disability (ID) and are strongly associated with autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD) and schizophrenia (SCZ). Here, we report the generation and characterization of mice harboring a null Upf3b allele. These Upf3b-null mice exhibit deficits in fear-conditioned learning, but not spatial learning. Upf3b-null mice also have a profound defect in prepulse inhibition (PPI), a measure of sensorimotor gating commonly deficient in individuals with SCZ and other brain disorders. Consistent with both their PPI and learning defects, cortical pyramidal neurons from Upf3b-null mice display deficient dendritic spine maturation in vivo. In addition, neural stem cells from Upf3b-null mice have impaired ability to undergo differentiation and require prolonged culture to give rise to functional neurons with electrical activity. RNA sequencing (RNAseq) analysis of the frontal cortex identified UPF3B-regulated RNAs, including direct NMD target transcripts encoding proteins with known functions in neural differentiation, maturation and disease. We suggest Upf3b-null mice serve as a novel model system to decipher cellular and molecular defects underlying ID and neurodevelopmental disorders.
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Affiliation(s)
- L Huang
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - E Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - S H Jones
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - C-H Lou
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - J Chousal
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - H Kim
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - A J Roberts
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - L A Jolly
- Adelaide Medical School and Robison Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - J L Espinoza
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - D M Skarbrevik
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - M H Phan
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - H Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - N R Swerdlow
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J Gecz
- Adelaide Medical School and Robison Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - M F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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30
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Rao S, Amorim R, Niu M, Temzi A, Mouland AJ. The RNA surveillance proteins UPF1, UPF2 and SMG6 affect HIV-1 reactivation at a post-transcriptional level. Retrovirology 2018; 15:42. [PMID: 29954456 PMCID: PMC6022449 DOI: 10.1186/s12977-018-0425-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/06/2018] [Indexed: 11/24/2022] Open
Abstract
Background The ability of human immunodeficiency virus type 1 (HIV-1) to form a stable viral reservoir is the major obstacle to an HIV-1 cure and post-transcriptional events contribute to the maintenance of viral latency. RNA surveillance proteins such as UPF1, UPF2 and SMG6 affect RNA stability and metabolism. In our previous work, we demonstrated that UPF1 stabilises HIV-1 genomic RNA (vRNA) and enhances its translatability in the cytoplasm. Thus, in this work we evaluated the influence of RNA surveillance proteins on vRNA expression and, as a consequence, viral reactivation in cells of the lymphoid lineage. Methods Quantitative fluorescence in situ hybridisation—flow cytometry (FISH-flow), si/shRNA-mediated depletions and Western blotting were used to characterise the roles of RNA surveillance proteins on HIV-1 reactivation in a latently infected model T cell line and primary CD4+ T cells. Results UPF1 was found to be a positive regulator of viral reactivation, with a depletion of UPF1 resulting in impaired vRNA expression and viral reactivation. UPF1 overexpression also modestly enhanced vRNA expression and its ATPase activity and N-terminal domain were necessary for this effect. UPF2 and SMG6 were found to negatively influence viral reactivation, both via an interaction with UPF1. UPF1 knockdown also resulted in reduced vRNA levels and viral gene expression in HIV-1-infected primary CD4+ T cells. Conclusion Overall, these data suggest that RNA surveillance proteins affect HIV-1 gene expression at a post-transcriptional level. An elucidation of the role of vRNA metabolism on the maintenance of HIV-1 persistence can lead to the development of novel curative strategies. Electronic supplementary material The online version of this article (10.1186/s12977-018-0425-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Raquel Amorim
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.,Department of Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
| | - Abdelkrim Temzi
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montreal, QC, H3T 1E2, Canada. .,Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada. .,Department of Medicine, McGill University, Montreal, QC, H3A 0G4, Canada.
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31
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Szádeczky-Kardoss I, Csorba T, Auber A, Schamberger A, Nyikó T, Taller J, Orbán TI, Burgyán J, Silhavy D. The nonstop decay and the RNA silencing systems operate cooperatively in plants. Nucleic Acids Res 2018; 46:4632-4648. [PMID: 29672715 PMCID: PMC5961432 DOI: 10.1093/nar/gky279] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here, we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which are produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. Here we show that NSD is required for the elimination of 5' cleavage product of mi- or siRNA-guided silencing complex when the cleavage occurs in the coding region. We also show that NSD and nonsense-mediated decay (NMD) quality control systems operate independently in plants.
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Affiliation(s)
| | - Tibor Csorba
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - János Taller
- University Pannonia Georgikon, Festetics 7, 8360 Keszthely, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - József Burgyán
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Dániel Silhavy
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
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32
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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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33
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Nakajima J, Oana S, Sakaguchi T, Nakashima M, Numabe H, Kawashima H, Matsumoto N, Miyake N. Novel compound heterozygous DPH1 mutations in a patient with the unique clinical features of airway obstruction and external genital abnormalities. J Hum Genet 2018; 63:529-532. [DOI: 10.1038/s10038-017-0399-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/07/2017] [Accepted: 11/19/2017] [Indexed: 01/11/2023]
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34
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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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35
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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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36
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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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37
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Plank T, Wilkinson MF. RNA Decay Factor UPF1 Promotes Protein Decay: A Hidden Talent. Bioessays 2018; 40:10.1002/bies.201700170. [PMID: 29236296 PMCID: PMC5843485 DOI: 10.1002/bies.201700170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/19/2017] [Indexed: 11/12/2022]
Abstract
The RNA-binding protein, UPF1, is best known for its central role in the nonsense-mediated RNA decay (NMD) pathway. Feng et al. now report a new function for UPF1-it is an E3 ubiquitin ligase that specifically promotes the decay of a key pro-muscle transcription factor: MYOD. UPF1 achieves this through its RING-like domain, which confers ubiquitin E3 ligase activity. Feng et al. provide evidence that the ability of UPF1 to destabilize MYOD represses myogenesis. In the future, it will be important to define other protein substrates of UPF1-driven ubiquitination and to determine whether this biochemical activity is responsible for some of UPF1's previously defined biological functions, including in development and stress responses. The exciting findings presented by Feng et al. open up the possibility that protein turnover and RNA turnover are coupled processes.
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Affiliation(s)
- Terra Plank
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093-0695, USA
| | - Miles F. Wilkinson
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093-0695, USA
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38
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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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Lou CH, Chousal J, Goetz A, Shum EY, Brafman D, Liao X, Mora-Castilla S, Ramaiah M, Cook-Andersen H, Laurent L, Wilkinson MF. Nonsense-Mediated RNA Decay Influences Human Embryonic Stem Cell Fate. Stem Cell Reports 2017; 6:844-857. [PMID: 27304915 PMCID: PMC4912386 DOI: 10.1016/j.stemcr.2016.05.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 11/18/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than in differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-β and BMP signaling, which we found NMD acts through to influence definitive endoderm versus mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages. The NMD RNA degradation pathway is highly active in pluripotent cells RNA-seq analysis identifies mRNA targets of NMD in human embryonic stem cells NMD degrades mRNAs encoding TGF-β/BMP, WNT, and FGF signaling components NMD acts through signaling pathways to influence endoderm versus mesoderm cell fate
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Affiliation(s)
- Chih-Hong Lou
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Chousal
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexandra Goetz
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleen Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - David Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoyan Liao
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Louise Laurent
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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40
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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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41
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42
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Goetz AE, Wilkinson M. Stress and the nonsense-mediated RNA decay pathway. Cell Mol Life Sci 2017; 74:3509-3531. [PMID: 28503708 PMCID: PMC5683946 DOI: 10.1007/s00018-017-2537-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 01/09/2023]
Abstract
Cells respond to internal and external cellular stressors by activating stress-response pathways that re-establish homeostasis. If homeostasis is not achieved in a timely manner, stress pathways trigger programmed cell death (apoptosis) to preserve organism integrity. A highly conserved stress pathway is the unfolded protein response (UPR), which senses excessive amounts of unfolded proteins in the ER. While a physiologically beneficial pathway, the UPR requires tight regulation to provide a beneficial outcome and avoid deleterious consequences. Recent work has demonstrated that a conserved and highly selective RNA degradation pathway-nonsense-mediated RNA decay (NMD)-serves as a major regulator of the UPR pathway. NMD degrades mRNAs encoding UPR components to prevent UPR activation in response to innocuous ER stress. In response to strong ER stress, NMD is inhibited by the UPR to allow for a full-magnitude UPR response. Recent studies have indicated that NMD also has other stress-related functions, including promoting the timely termination of the UPR to avoid apoptosis; NMD also regulates responses to non-ER stressors, including hypoxia, amino-acid deprivation, and pathogen infection. NMD regulates stress responses in species across the phylogenetic scale, suggesting that it has conserved roles in shaping stress responses. Stress pathways are frequently constitutively activated or dysregulated in human disease, raising the possibility that "NMD therapy" may provide clinical benefit by downmodulating stress responses.
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Affiliation(s)
- Alexandra E Goetz
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, 9500 Gilman Dr., La Jolla, 92093, USA
| | - Miles Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, 9500 Gilman Dr., La Jolla, 92093, USA.
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43
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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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44
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Gerbracht JV, Boehm V, Gehring NH. Plasmid transfection influences the readout of nonsense-mediated mRNA decay reporter assays in human cells. Sci Rep 2017; 7:10616. [PMID: 28878343 PMCID: PMC5587671 DOI: 10.1038/s41598-017-10847-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/15/2017] [Indexed: 12/31/2022] Open
Abstract
Messenger RNA (mRNA) turnover is a crucial and highly regulated step of gene expression in mammalian cells. This includes mRNA surveillance pathways such as nonsense-mediated mRNA decay (NMD), which assesses the fidelity of transcripts and eliminates mRNAs containing a premature translation termination codon (PTC). When studying mRNA degradation pathways, reporter mRNAs are commonly expressed in cultivated cells. Traditionally, the molecular mechanism of NMD has been characterized using pairs of reporter constructs that express the same mRNA with (“PTC-containing mRNA”) or without (“wild-type mRNA”) a PTC. Cell lines stably expressing an NMD reporter have been reported to yield very robust and highly reproducible results, but establishing the cell lines can be very time-consuming. Therefore, transient transfection of such reporter constructs is frequently used and allows analysis of many samples within a short period of time. However, the behavior of transiently and stably transfected NMD constructs has not been systematically compared so far. Here, we report that not all commonly used human cell lines degrade NMD targets following transient transfection. Furthermore, the degradation efficiency of NMD substrates can depend on the manner of transfection within the same cell line. This has substantial implications for the interpretation of NMD assays based on transient transfections.
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Affiliation(s)
- Jennifer V Gerbracht
- Institute for Genetics, Department of Biology, University of Cologne, 50674, Cologne, Germany
| | - Volker Boehm
- Institute for Genetics, Department of Biology, University of Cologne, 50674, Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, Department of Biology, University of Cologne, 50674, Cologne, Germany.
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45
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Hoque M, Park JY, Chang YJ, Luchessi AD, Cambiaghi TD, Shamanna R, Hanauske-Abel HM, Holland B, Pe'ery T, Tian B, Mathews MB. Regulation of gene expression by translation factor eIF5A: Hypusine-modified eIF5A enhances nonsense-mediated mRNA decay in human cells. ACTA ACUST UNITED AC 2017; 5:e1366294. [PMID: 29034140 DOI: 10.1080/21690731.2017.1366294] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/28/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) couples protein synthesis to mRNA turnover. It eliminates defective transcripts and controls the abundance of certain normal mRNAs. Our study establishes a connection between NMD and the translation factor eIF5A (eukaryotic initiation factor 5A) in human cells. eIF5A modulates the synthesis of groups of proteins (the eIF5A regulon), and undergoes a distinctive two-step post-translational modification (hypusination) catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase. We show that expression of NMD-susceptible constructs was increased by depletion of the major eIF5A isoform, eIF5A1. NMD was also attenuated when hypusination was inhibited by RNA interference with either of the two eIF5A modifying enzymes, or by treatment with the drugs ciclopirox or deferiprone which inhibit deoxyhypusine hydroxylase. Transcriptome analysis by RNA-Seq identified human genes whose expression is coordinately regulated by eIF5A1, its modifying enzymes, and the pivotal NMD factor, Upf1. Transcripts encoding components of the translation system were highly represented, including some encoding ribosomal proteins controlled by alternative splicing coupled to NMD (AS-NMD). Our findings extend and strengthen the association of eIF5A with NMD, previously inferred in yeast, and show that hypusination is important for this function of human eIF5A. In addition, they advance drug-mediated NMD suppression as a therapeutic opportunity for nonsense-associated diseases. We propose that regulation of mRNA stability contributes to eIF5A's role in selective gene expression.
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Affiliation(s)
- Mainul Hoque
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ji Yeon Park
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Yun-Juan Chang
- Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA.,Office of Advanced Research Computing, Rutgers University, Newark, NJ, USA
| | - Augusto D Luchessi
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA.,Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
| | - Tavane D Cambiaghi
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Raghavendra Shamanna
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Hartmut M Hanauske-Abel
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bart Holland
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Tsafi Pe'ery
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Michael B Mathews
- Department of Biochemistry & Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
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46
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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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47
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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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48
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Up-Frameshift Protein UPF1 Regulates Neurospora crassa Circadian and Diurnal Growth Rhythms. Genetics 2017; 206:1881-1893. [PMID: 28600326 DOI: 10.1534/genetics.117.202788] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 05/31/2017] [Indexed: 01/24/2023] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a crucial post-transcriptional regulatory mechanism that recognizes and eliminates aberrantly processed transcripts, and mediates the expression of normal gene transcripts. In this study, we report that in the filamentous fungus Neurospora crassa, the NMD factors play a conserved role in regulating the surveillance of NMD targets including premature termination codon (PTC)-containing transcripts and normal transcripts. The circadian rhythms in all of the knockout strains of upf1-3 genes, which encode the Up-frameshift proteins, were aberrant. The upf1 knockout strain displays a shortened circadian period, which can be restored by constantly expressing exogenous Up-frameshift protein 1 (UPF1). UPF1 regulates the circadian clock by modulating the splicing of the core clock gene frequency (frq) through spliceosome and spliceosome-related arginine/serine-rich splicing factors, which partly account for the short periods in the upf1 knockout strain. We also demonstrated that the clock genes including White Collar (WC)-1, WC-2, and FRQ are involved in controlling the diurnal growth rhythm, and UPF1 may affect the growth rhythms by mediating the FRQ protein levels in the daytime. These findings suggest that the NMD factors play important roles in regulating the circadian clock and diurnal growth rhythms in Neurospora.
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49
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Park J, Park Y, Ryu I, Choi MH, Lee HJ, Oh N, Kim K, Kim KM, Choe J, Lee C, Baik JH, Kim YK. Misfolded polypeptides are selectively recognized and transported toward aggresomes by a CED complex. Nat Commun 2017; 8:15730. [PMID: 28589942 PMCID: PMC5467238 DOI: 10.1038/ncomms15730] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
Misfolded polypeptides are rapidly cleared from cells via the ubiquitin–proteasome system (UPS). However, when the UPS is impaired, misfolded polypeptides form small cytoplasmic aggregates, which are sequestered into an aggresome and ultimately degraded by aggrephagy. Despite the relevance of the aggresome to neurodegenerative proteinopathies, the molecular mechanisms underlying aggresome formation remain unclear. Here we show that the CTIF–eEF1A1–DCTN1 (CED) complex functions in the surveillance of either pre-existing or newly synthesized polypeptides by linking two molecular events: selective recognition and aggresomal targeting of misfolded polypeptides. These events are accompanied by CTIF sequestration into the aggresome, preventing the additional synthesis of misfolded polypeptides from mRNAs bound by nuclear cap-binding complex. These events render cells more resistant to apoptosis induced by proteotoxic stresses. Collectively, our data provide compelling evidence for a previously unappreciated protein surveillance pathway and a regulatory gene expression network for coping with misfolded polypeptides. Misfolded polypeptide aggregates are actively transported to aggresomes, where they are degraded through aggrephagy. Here the authors show that these aggregates are selectively recognized by the CTIF–eEF1A1–DCTN1 (CED) complex and transported to aggresomes through the interactions of DCTN1 with dynein motors.
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Affiliation(s)
- 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
| | - Yeonkyoung 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
| | - Incheol Ryu
- 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
| | - Mi-Hyun Choi
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyo Jin Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Nara Oh
- 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
| | - Kyutae Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea.,BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Kyoung Mi Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Junho Choe
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Cheolju Lee
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Ja-Hyun Baik
- 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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Fukao A, Fujiwara T. The coupled and uncoupled mechanisms by which trans-acting factors regulate mRNA stability and translation. J Biochem 2017; 161:309-314. [PMID: 28039391 DOI: 10.1093/jb/mvw086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 12/25/2022] Open
Abstract
In mammals, spatiotemporal control of protein synthesis plays a key role in the post-transcriptional regulation of gene expression during cell proliferation, development and differentiation and RNA-binding proteins (RBPs) and microRNAs (miRNAs) are required for this phenomenon. RBPs and miRNAs control the levels of mRNA protein products by regulating mRNA stability and translation. Recent studies have shown that RBPs and miRNAs simultaneously regulate mRNA stability and translation, and that the differential functions of RBPs and miRNAs are dependent on their interaction partners. Here, we summarize the coupled- and uncoupled mechanisms by which trans-acting factors regulate mRNA stability and translation.
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