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Ma Z, Sharma R, Rogers AN. Physiological Consequences of Nonsense-Mediated Decay and Its Role in Adaptive Responses. Biomedicines 2024; 12:1110. [PMID: 38791071 PMCID: PMC11117581 DOI: 10.3390/biomedicines12051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway is a quality control mechanism that degrades aberrant mRNA containing one or more premature termination codons (PTCs). Recent discoveries indicate that NMD also differentially regulates mRNA from wild-type protein-coding genes despite lacking PTCs. Together with studies showing that NMD is involved in development and adaptive responses that influence health and longevity, these findings point to an expanded role of NMD that adds a new layer of complexity in the post-transcriptional regulation of gene expression. However, the extent of its control, whether different types of NMD play different roles, and the resulting physiological outcomes remain unclear and need further elucidation. Here, we review different branches of NMD and what is known of the physiological outcomes associated with this type of regulation. We identify significant gaps in the understanding of this process and the utility of genetic tools in accelerating progress in this area.
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Affiliation(s)
- Zhengxin Ma
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ratna Sharma
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA;
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2
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Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3'UTR. NMD detects such mRNAs and rapidly degrades them during initial rounds of translation in the eukaryotic cells. Since NMD is a translation-dependent cytoplasmic mRNA surveillance process, the noncoding RNAs were initially believed to be NMD-resistant. The sequence feature-based analysis has revealed that many putative long noncoding RNAs (lncRNAs) have short open reading frames, most of which have translation potential. Subsequent transcriptome-based molecular studies showed an association of a large set of such putative lncRNAs with translating ribosomes, and some of them produce stable and functionally active micropeptides. The translationally active lncRNAs typically have relatively longer and unprotected 3'UTR, which can induce their NMD-dependent degradation. This review defines the mechanism and regulation of NMD-dependent degradation of lncRNAs and its impact on biological processes related to the functions of lncRNAs or their encoded micropeptides. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anand Kumar Singh
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
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3
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Lin L, Zhao J, Kubota N, Li Z, Lam YL, Nguyen LP, Yang L, Pokharel SP, Blue SM, Yee BA, Chen R, Yeo GW, Chen CW, Chen L, Zheng S. Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. Neuron 2024:S0896-6273(24)00244-7. [PMID: 38697111 DOI: 10.1016/j.neuron.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/14/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's critical roles in progenitors. Upf2 knockout (KO) prolongs the cell cycle of radial glia progenitor cells, promotes their transition into intermediate progenitors, and leads to reduced upper-layer neurons. CRISPRi screening identified Trp53 knockdown rescuing Upf2KO progenitors without globally reversing NMD inhibition, implying marginal contributions of most NMD targets to the cell cycle defect. Integrated functional genomics shows that NMD degrades selective TRP53 downstream targets, including Cdkn1a, which, without NMD suppression, slow the cell cycle. Trp53KO restores the progenitor cell pool and rescues the microcephaly of Upf2KO mice. Therefore, one physiological role of NMD in the developing brain is to degrade selective TRP53 targets to control progenitor cell cycle and brain size.
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Affiliation(s)
- Lin Lin
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Jingrong Zhao
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Naoto Kubota
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Zhelin Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Yi-Li Lam
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Lauren P Nguyen
- Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela P Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA; City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA; Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA.
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4
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Kolakada D, Campbell AE, Galvis LB, Li Z, Lore M, Jagannathan S. A system of reporters for comparative investigation of EJC-independent and EJC-enhanced nonsense-mediated mRNA decay. Nucleic Acids Res 2024; 52:e34. [PMID: 38375914 PMCID: PMC11014337 DOI: 10.1093/nar/gkae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/05/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a network of pathways that degrades transcripts that undergo premature translation termination. In mammals, NMD can be divided into the exon junction complex (EJC)-enhanced and EJC-independent branches. Fluorescence- and luminescence-based reporters have long been effective tools to investigate NMD, yet existing reporters largely focus on the EJC-enhanced pathway. Here, we present a system of reporters for comparative studies of EJC-independent and EJC-enhanced NMD. This system also enables the study of NMD-associated outcomes such as premature termination codon (PTC) readthrough and truncated protein degradation. These reporters are compatible with fluorescence or luminescence-based readouts via transient transfection or stable integration. Using this reporter system, we show that EJC-enhanced NMD RNA levels are reduced by 2- or 9-fold and protein levels are reduced by 7- or 12-fold compared to EJC-independent NMD, depending on the reporter gene used. Additionally, the extent of readthrough induced by G418 and an NMD inhibitor (SMG1i), alone and in combination, varies across NMD substrates. When combined, G418 and SMG1i increase readthrough product levels in an additive manner for EJC-independent reporters, while EJC-enhanced reporters show a synergistic effect. We present these reporters as a valuable toolkit to deepen our understanding of NMD and its associated mechanisms.
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Affiliation(s)
- Divya Kolakada
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amy E Campbell
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Laura Baquero Galvis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhongyou Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mlana Lore
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, 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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5
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Das R, Panigrahi GK. Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications. Mol Biotechnol 2024:10.1007/s12033-024-01062-4. [PMID: 38411790 DOI: 10.1007/s12033-024-01062-4] [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: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism in eukaryotes primarily deployed to ensure RNA quality control by eliminating aberrant transcripts and also involved in modulating the expression of several physiological transcripts. NMD, the mRNA surveillance pathway, is a major form of gene regulation in eukaryotes. NMD serves as one of the most significant quality control mechanisms as it primarily scans the newly synthesized transcripts and differentiates the aberrant and non-aberrant transcripts. The synthesis of truncated proteins is restricted, which would otherwise lead to cellular dysfunctions. The up-frameshift factors (UPFs) play a central role in executing the NMD event, largely by recognizing and recruiting multiple protein factors that result in the decay of non-physiological mRNAs. NMD exhibits astounding variability in its ability across eukaryotes in an array of pathological and physiological contexts. The detailed understanding of NMD and the underlying molecular mechanisms remains blurred. This review outlines our current understanding of NMD, in regulating multifaceted cellular events during development and disease. It also attempts to identify unanswered questions that deserve further investigation.
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Affiliation(s)
- Rutupurna Das
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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6
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Gomez N, Hsieh C, Li X, Dykstra M, Waksmacki J, Altheim C, Bechar Y, Klim J, Zaepfel B, Rothstein J, Tank EE, Barmada SJ. Counter-regulation of RNA stability by UPF1 and TDP43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578310. [PMID: 38352350 PMCID: PMC10862862 DOI: 10.1101/2024.01.31.578310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
RNA quality control is crucial for proper regulation of gene expression. Disruption of nonsense mediated mRNA decay (NMD), the primary RNA decay pathway responsible for the degradation of transcripts containing premature termination codons (PTCs), can disrupt development and lead to multiple diseases in humans and other animals. Similarly, therapies targeting NMD may have applications in hematological, neoplastic and neurological disorders. As such, tools capable of accurately quantifying NMD status could be invaluable for investigations of disease pathogenesis and biomarker identification. Toward this end, we assemble, validate, and apply a next-generation sequencing approach (NMDq) for identifying and measuring the abundance of PTC-containing transcripts. After validating NMDq performance and confirming its utility for tracking RNA surveillance, we apply it to determine pathway activity in two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) characterized by RNA misprocessing and abnormal RNA stability. Despite the genetic and pathologic evidence implicating dysfunctional RNA metabolism, and NMD in particular, in these conditions, we detected no significant differences in PTC-encoding transcripts in ALS models or disease. Contrary to expectations, overexpression of the master NMD regulator UPF1 had little effect on the clearance of transcripts with PTCs, but rather restored RNA homeostasis through differential use and decay of alternatively poly-adenylated isoforms. Together, these data suggest that canonical NMD is not a significant contributor to ALS/FTD pathogenesis, and that UPF1 promotes neuronal survival by regulating transcripts with abnormally long 3'UTRs.
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Jung S, Ko SH, Ahn N, Lee J, Park CH, Hwang J. Role of UPF1-LIN28A interaction during early differentiation of pluripotent stem cells. Nat Commun 2024; 15:158. [PMID: 38167913 PMCID: PMC10762078 DOI: 10.1038/s41467-023-44600-5] [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: 02/13/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
UPF1 and LIN28A are RNA-binding proteins involved in post-transcriptional regulation and stem cell differentiation. Most studies on UPF1 and LIN28A have focused on the molecular mechanisms of differentiated cells and stem cell differentiation, respectively. We reveal that LIN28A directly interacts with UPF1 before UPF1-UPF2 complexing, thereby reducing UPF1 phosphorylation and inhibiting nonsense-mediated mRNA decay (NMD). We identify the interacting domains of UPF1 and LIN28A; moreover, we develop a peptide that impairs UPF1-LIN28A interaction and augments NMD efficiency. Transcriptome analysis of human pluripotent stem cells (hPSCs) confirms that the levels of NMD targets are significantly regulated by both UPF1 and LIN28A. Inhibiting the UPF1-LIN28A interaction using a CPP-conjugated peptide promotes spontaneous differentiation by repressing the pluripotency of hPSCs during proliferation. Furthermore, the UPF1-LIN28A interaction specifically regulates transcripts involved in ectodermal differentiation. Our study reveals that transcriptome regulation via the UPF1-LIN28A interaction in hPSCs determines cell fate.
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Affiliation(s)
- Seungwon Jung
- Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Seung Hwan Ko
- Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Narae Ahn
- Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Jinsam Lee
- Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Chang-Hwan Park
- Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea.
| | - Jungwook Hwang
- Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea.
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Korea.
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8
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Carrard J, Lejeune F. Nonsense-mediated mRNA decay, a simplified view of a complex mechanism. BMB Rep 2023; 56:625-632. [PMID: 38052423 PMCID: PMC10761751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a quality control mechanism and a gene regulation pathway. It has been studied for more than 30 years, with an accumulation of many mechanistic details that have often led to debate and hence to different models of NMD activation, particularly in higher eukaryotes. Two models seem to be opposed, since the first requires intervention of the exon junction complex (EJC) to recruit NMD factors downstream of the premature termination codon (PTC), whereas the second involves an EJC-independent mechanism in which NMD factors concentrate in the 3'UTR to initiate NMD in the presence of a PTC. In this review we describe both models, giving recent molecular details and providing experimental arguments supporting one or the other model. In the end it is certainly possible to imagine that these two mechanisms co-exist, rather than viewing them as mutually exclusive. [BMB Reports 2023; 56(12): 625-632].
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Affiliation(s)
- Julie Carrard
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
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9
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Kolakada D, Campbell AE, Baquero Galvis L, Li Z, Lore M, Jagannathan S. A system of reporters for comparative investigation of EJC-independent and EJC-enhanced nonsense-mediated mRNA decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567061. [PMID: 38014198 PMCID: PMC10680754 DOI: 10.1101/2023.11.14.567061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a network of pathways that degrades transcripts that undergo premature translation termination. In mammals, NMD can be divided into the exon junction complex (EJC)-enhanced and EJC-independent branches. Fluorescence- and luminescence-based reporters have long been effective tools to investigate NMD, yet existing reporters largely focus on the EJC-enhanced pathway. Here, we present a system of reporters for comparative studies of EJC-independent and EJC-enhanced NMD. This system also enables the study of NMD-associated outcomes such as premature termination codon (PTC) readthrough and truncated protein degradation. These reporters are compatible with fluorescence or luminescence-based readouts via transient transfection or stable integration. Using this reporter system, we show that EJC-enhanced NMD RNA levels are reduced by 2- or 9-fold and protein levels are reduced by 7- or 12-fold compared to EJC-independent NMD, depending on the reporter gene used. Additionally, the extent of readthrough induced by G418 and SMG1i, alone and in combination, varies across NMD substrates. When combined, G418 and SMG1i increase readthrough product levels in an additive manner for EJC-independent reporters, while EJC-enhanced reporters show a synergistic effect. We present these reporters as a valuable toolkit to deepen our understanding of NMD and its associated mechanisms.
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Affiliation(s)
- Divya Kolakada
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amy E. Campbell
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Laura Baquero Galvis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhongyou Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mlana Lore
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, 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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Siddiqui A, Saxena A, Echols J, Havasi V, Fu L, Keeling KM. RNA binding proteins PTBP1 and HNRNPL regulate CFTR mRNA decay. Heliyon 2023; 9:e22281. [PMID: 38045134 PMCID: PMC10692906 DOI: 10.1016/j.heliyon.2023.e22281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
Background CFTR nonsense alleles generate negligible CFTR protein due to the nonsense mutation: 1) triggering CFTR mRNA degradation by nonsense-mediated mRNA decay (NMD), and 2) terminating CFTR mRNA translation prematurely. Thus, people with cystic fibrosis (PwCF) who carry nonsense alleles cannot benefit from current modulator drugs, which target CFTR protein. In this study, we examined whether PTBP1 and HNRNPL, two RNA binding proteins that protect a subset of mRNAs with a long 3' untranslated region (UTR) from NMD, similarly affect CFTR mRNA.Silencing RNAs were used to deplete PTBP1 or HNRNPL in 16HBE14o- human bronchial epithelial cells expressing WT, G542X, or W1282X CFTR. CFTR mRNA abundance was measured relative to controls by quantitative PCR. PTBP1 and HNRNPL were also exogenously expressed in each cell line and CFTR mRNA levels were similarly quantified. Results PTBP1 depletion reduced CFTR mRNA abundance in all three 16HBE14o- cell lines; HRNPL depletion reduced CFTR mRNA abundance in only the G542X and W1282X cell lines. Notably, decreased CFTR mRNA abundance correlated with increased mRNA decay. Exogenous expression of PTBP1 or HNRNPL increased CFTR mRNA abundance in all three cell lines; HNRNPL overexpression generally increased CFTR to a greater extent in G542X and W1282X 16HBE14o- cells.Our data indicate that PTBP1 and HNRNPL regulate CFTR mRNA abundance by protecting CFTR transcripts from NMD. This suggests that PTBP1 and/or HNRNPL may represent potential therapeutic targets to increase CFTR mRNA abundance and enhance responses to CFTR modulators and other therapeutic approaches in PwCF.
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Affiliation(s)
- Amna Siddiqui
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
- Comprehensive Cancer Center and, USA
| | - Arpit Saxena
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Joshua Echols
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
- Department of Pediatrics, Infectious Diseases Division, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Viktoria Havasi
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
- Comprehensive Cancer Center and, USA
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Biochemistry and Molecular Genetics and, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
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11
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Petrić Howe M, Patani R. Nonsense-mediated mRNA decay in neuronal physiology and neurodegeneration. Trends Neurosci 2023; 46:879-892. [PMID: 37543480 DOI: 10.1016/j.tins.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/19/2023] [Accepted: 07/09/2023] [Indexed: 08/07/2023]
Abstract
The processes of mRNA export from the nucleus and subsequent mRNA translation in the cytoplasm are of particular relevance in eukaryotic cells. In highly polarised cells such as neurons, finely-tuned molecular regulation of these processes serves to safeguard the spatiotemporal fidelity of gene expression. Nonsense-mediated mRNA decay (NMD) is a cytoplasmic translation-dependent quality control process that regulates gene expression in a wide range of scenarios in the nervous system, including neurodevelopment, learning, and memory formation. Moreover, NMD dysregulation has been implicated in a broad range of neurodevelopmental and neurodegenerative disorders. We discuss how NMD and related aspects of mRNA translation regulate key neuronal functions and, in particular, we focus on evidence implicating these processes in the molecular pathogenesis of neurodegeneration. Finally, we discuss the therapeutic potential and challenges of targeting mRNA translation and NMD across the spectrum of largely untreatable neurological diseases.
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Affiliation(s)
- Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London (UCL), Queen Square, WC1N 3BG London, UK.
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London (UCL), Queen Square, WC1N 3BG London, UK.
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12
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Lee S, Jung H, Choi S, Cho N, Kim EM, Kim KK. Intron retention decreases METTL3 expression by inhibiting mRNA export to the cytoplasm. BMB Rep 2023; 56:514-519. [PMID: 37357537 PMCID: PMC10547966 DOI: 10.5483/bmbrep.2023-0069] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/20/2023] [Accepted: 06/20/2023] [Indexed: 10/19/2023] Open
Abstract
Methyltransferase-like 3 (METTL3), a key component of the m6A methyltransferase complex, regulates the splicing, nuclear transport, stability, and translation of its target genes. However, the mechanism underlying the regulation of METTL3 expression by alternative splicing (AS) remains unknown. We analyzed the expression pattern of METTL3 after AS in human tissues and confirmed the expression of an isoform retaining introns 8 and 9 (METTL3-IR). We confirmed the different intracellular localizations of METTL3-IR and METTL3 proteins using immunofluorescence microscopy. Furthermore, the endogenous expression of METTL3-IR at the protein level was different from that at the mRNA level. We found that 3'-UTR generation by intron retention (IR) inhibited the export of METTL3-IR mRNA to the cytoplasm, which in turn suppressed protein expression. To the best of our knowledge, this is the first study to confirm the regulation of METTL3 gene expression by AS, providing evidence that the suppression of METTL3 protein expression by IR is an integral part of the mechanism by which 3'-UTR generation regulates protein expression via inhibition of RNA export to the cytoplasm. [BMB Reports 2023; 56(9): 514-519].
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Affiliation(s)
- Sangsoo Lee
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Haesoo Jung
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea
| | - Kee Kwang Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
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13
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Lee S, Jung H, Choi S, Cho N, Kim EM, Kim KK. Intron retention decreases METTL3 expression by inhibiting mRNA export to the cytoplasm. BMB Rep 2023; 56:514-519. [PMID: 37357537 PMCID: PMC10547966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/20/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023] Open
Abstract
Methyltransferase-like 3 (METTL3), a key component of the m6A methyltransferase complex, regulates the splicing, nuclear transport, stability, and translation of its target genes. However, the mechanism underlying the regulation of METTL3 expression by alternative splicing (AS) remains unknown. We analyzed the expression pattern of METTL3 after AS in human tissues and confirmed the expression of an isoform retaining introns 8 and 9 (METTL3-IR). We confirmed the different intracellular localizations of METTL3-IR and METTL3 proteins using immunofluorescence microscopy. Furthermore, the endogenous expression of METTL3-IR at the protein level was different from that at the mRNA level. We found that 3'-UTR generation by intron retention (IR) inhibited the export of METTL3-IR mRNA to the cytoplasm, which in turn suppressed protein expression. To the best of our knowledge, this is the first study to confirm the regulation of METTL3 gene expression by AS, providing evidence that the suppression of METTL3 protein expression by IR is an integral part of the mechanism by which 3'-UTR generation regulates protein expression via inhibition of RNA export to the cytoplasm. [BMB Reports 2023; 56(9): 514-519].
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Affiliation(s)
- Sangsoo Lee
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Haesoo Jung
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea
| | - Kee Kwang Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Korea
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14
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Steiner AJ, Zheng Y, Tang Y. Characterization of a rhabdomyosarcoma reveals a critical role for SMG7 in cancer cell viability and tumor growth. Sci Rep 2023; 13:10152. [PMID: 37349371 PMCID: PMC10287741 DOI: 10.1038/s41598-023-36568-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
Soft-tissue sarcomas (STSs) are a rare and diverse group of mesenchymal cancers plagued with aggression, poor response to systemic therapy, and high rates of recurrence. Although STSs generally have low mutational burdens, the most commonly mutated genes are tumor suppressors, which frequently acquire mutations inducing nonsense-mediated mRNA decay (NMD). This suggests that STS cells may exploit NMD to suppress these anti-cancer genes. To examine the role that the NMD factor SMG7 plays in STS, we developed an inducible knockout mouse model in the Trp53-/- background. Here, we isolated a subcutaneous STS and identified it as a rhabdomyosarcoma (RMS). We report that knockout of SMG7 significantly inhibited NMD in our RMS cells, which led to the induction of NMD targets GADD45b and the tumor suppressor GAS5. The loss of NMD and upregulation of these anti-cancer genes were concomitant with the loss of RMS cell viability and inhibited tumor growth. Importantly, SMG7 was dispensable for homeostasis in our mouse embryonic fibroblasts and adult mice. Overall, our data show that the loss of SMG7 induces a strong anti-cancer effect both in vitro and in vivo. We present here the first evidence that disrupting SMG7 function may be tolerable and provide a therapeutic benefit for STS treatment.
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Affiliation(s)
- Alexander J Steiner
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue, Albany, NY, 12208, USA
| | - Yang Zheng
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue, Albany, NY, 12208, USA
| | - Yi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue, Albany, NY, 12208, USA.
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15
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Xiong W, Li D, Feng Y, Jia C, Zhang X, Liu Z. CircLPAR1 Promotes Neuroinflammation and Oxidative Stress in APP/PS1 Mice by Inhibiting SIRT1/Nrf-2/HO-1 Axis Through Destabilizing GDF-15 mRNA. Mol Neurobiol 2023; 60:2236-2251. [PMID: 36646968 DOI: 10.1007/s12035-022-03177-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
Circular RNA LPAR1 (circLPAR1) was revealed to be elevated in Alzheimer's disease (AD); nevertheless, its role and mechanisms in AD remain unknown. Memory performance of APP/PS1 mice was assessed by Morris water maze test. Expression of circLPAR1 and indicated messenger RNA (mRNA) in mouse brain tissues or/and SH-SY5Y cells were tested by quantitative real-time PCR (qRT-PCR). Protein expression of indicated gene was examined by western blot. Production of proinflammatory cytokines (tumor necrosis factor-α, TNF-α; interleukin-6, IL-6; interleukin-1β, IL-1β; and interleukin-8, IL-8) and oxidative stress-related factors (reactive oxygen species, ROS; malondialdehyde, MDA; superoxide dismutase, SOD; and glutathione, GSH) were assessed by commercial kits. RNA pull down and RNA immunoprecipitation were performed to verify the interplay between up-frameshift protein 1 (UPF1) and circLPAR1 or growth differentiation factor 15 (GDF-15). CircLPAR1 was elevated, while GDF-15 was decreased in both APP/PS1 mice and Aβ-treated SH-SY5Y cells. Knockdown of circLPAR1 and overexpression of GDF-15 protected cells against Aβ-caused inflammation, oxidative stress, and neuronal apoptosis. CircLPAR1 knockdown was also proved to improve AD-related pathological traits and ameliorate cognitive dysfunctions in vivo. In mechanism, we found that circLPAR1 repressed GDF-15 expression by decreasing GDF-15 mRNA stability through UPF1 recruitment. Rescue assays suggested that sirtuin 1 (SIRT1) knockdown reversed GDF-15 overexpression-induced inhibition on Aβ-induced neuronal damage and nuclear factor E2-related factor (Nrf-2)/heme oxygenase-1 (HO-1) pathway inhibition. Moreover, the protective effect of circLPAR1 knockdown against Aβ-induced apoptosis was abolished by GDF-15 knockdown, and SIRT1 overexpression could counteract this effect of GDF-15 knockdown. CircLPAR1 knockdown improved AD-related pathological traits in vitro and in vivo by inhibiting SIRT1/Nrf-2/HO-1 axis through GDF-15.
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Affiliation(s)
- Wenping Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Dongming Li
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Yu Feng
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Chenguang Jia
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Xiangyu Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Zheng Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, No. 169, East Lake Road, Wuchang District, Wuhan, 430071, Hubei Province, People's Republic of China.
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16
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The biological functions of nonsense-mediated mRNA decay in plants: RNA quality control and beyond. Biochem Soc Trans 2023; 51:31-39. [PMID: 36695509 DOI: 10.1042/bst20211231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved quality control pathway that inhibits the expression of transcripts containing premature termination codon. Transcriptome and phenotypic studies across a range of organisms indicate roles of NMD beyond RNA quality control and imply its involvement in regulating gene expression in a wide range of physiological processes. Studies in moss Physcomitrella patens and Arabidopsis thaliana have shown that NMD is also important in plants where it contributes to the regulation of pathogen defence, hormonal signalling, circadian clock, reproduction and gene evolution. Here, we provide up to date overview of the biological functions of NMD in plants. In addition, we discuss several biological processes where NMD factors implement their function through NMD-independent mechanisms.
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17
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Sun L, Mailliot J, Schaffitzel C. Nonsense-Mediated mRNA Decay Factor Functions in Human Health and Disease. Biomedicines 2023; 11:722. [PMID: 36979701 PMCID: PMC10045457 DOI: 10.3390/biomedicines11030722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance mechanism that degrades mRNAs with a premature stop codon, avoiding the synthesis of C-terminally truncated proteins. In addition to faulty mRNAs, NMD recognises ~10% of endogenous transcripts in human cells and downregulates their expression. The up-frameshift proteins are core NMD factors and are conserved from yeast to human in structure and function. In mammals, NMD diversified into different pathways that target different mRNAs employing additional NMD factors. Here, we review our current understanding of molecular mechanisms and cellular roles of NMD pathways and the involvement of more specialised NMD factors. We describe the consequences of mutations in NMD factors leading to neurodevelopmental diseases, and the role of NMD in cancer. We highlight strategies of RNA viruses to evade recognition and decay by the NMD machinery.
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Affiliation(s)
- Lingling Sun
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Justine Mailliot
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
- Bristol Engineering Biology Centre BrisEngBio, 24 Tyndall Ave, Bristol BS8 1TQ, UK
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18
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Zuniga G, Levy S, Ramirez P, Mange JD, Gonzalez E, Gamez M, Frost B. Tau-induced deficits in nonsense-mediated mRNA decay contribute to neurodegeneration. Alzheimers Dement 2023; 19:405-420. [PMID: 35416419 PMCID: PMC9673995 DOI: 10.1002/alz.12653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/26/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION While brains of patients with Alzheimer's disease and related tauopathies have evidence of altered RNA processing, we lack a mechanistic understanding of how altered RNA processing arises in these disorders and if such changes are causally linked to neurodegeneration. METHODS Using Drosophila melanogaster models of tauopathy, we find that overall activity of nonsense-mediated mRNA decay (NMD), a key RNA quality-control mechanism, is reduced. Genetic manipulation of NMD machinery significantly modifies tau-induced neurotoxicity, suggesting that deficits in NMD are causally linked to neurodegeneration. Mechanistically, we find that deficits in NMD are a consequence of aberrant RNA export and RNA accumulation within nuclear envelope invaginations in tauopathy. We identify a pharmacological activator of NMD that suppresses neurodegeneration in tau transgenic Drosophila, indicating that tau-induced deficits in RNA quality control are druggable. DISCUSSION Our studies suggest that NMD activators should be explored for their potential therapeutic value to patients with tauopathies.
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Affiliation(s)
- Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Simon Levy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Jasmine De Mange
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Elias Gonzalez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Maria Gamez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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19
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Staszewski J, Lazarewicz N, Konczak J, Migdal I, Maciaszczyk-Dziubinska E. UPF1-From mRNA Degradation to Human Disorders. Cells 2023; 12:cells12030419. [PMID: 36766761 PMCID: PMC9914065 DOI: 10.3390/cells12030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Up-frameshift protein 1 (UPF1) plays the role of a vital controller for transcripts, ready to react in the event of an incorrect translation mechanism. It is well known as one of the key elements involved in mRNA decay pathways and participates in transcript and protein quality control in several different aspects. Firstly, UPF1 specifically degrades premature termination codon (PTC)-containing products in a nonsense-mediated mRNA decay (NMD)-coupled manner. Additionally, UPF1 can potentially act as an E3 ligase and degrade target proteins independently from mRNA decay pathways. Thus, UPF1 protects cells against the accumulation of misfolded polypeptides. However, this multitasking protein may still hide many of its functions and abilities. In this article, we summarize important discoveries in the context of UPF1, its involvement in various cellular pathways, as well as its structural importance and mutational changes related to the emergence of various pathologies and disease states. Even though the state of knowledge about this protein has significantly increased over the years, there are still many intriguing aspects that remain unresolved.
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Affiliation(s)
- Jacek Staszewski
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Institute of Genetics and Development of Rennes, CNRS UMR 6290, University of Rennes 1, 35000 Rennes, France
| | - Julia Konczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Iwona Migdal
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
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20
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Deng M, Wang X, Xiong Z, Tang P. Control of RNA degradation in cell fate decision. Front Cell Dev Biol 2023; 11:1164546. [PMID: 37025171 PMCID: PMC10070868 DOI: 10.3389/fcell.2023.1164546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cell fate is shaped by a unique gene expression program, which reflects the concerted action of multilayered precise regulation. Substantial research attention has been paid to the contribution of RNA biogenesis to cell fate decisions. However, increasing evidence shows that RNA degradation, well known for its function in RNA processing and the surveillance of aberrant transcripts, is broadly engaged in cell fate decisions, such as maternal-to-zygotic transition (MZT), stem cell differentiation, or somatic cell reprogramming. In this review, we first look at the diverse RNA degradation pathways in the cytoplasm and nucleus. Then, we summarize how selective transcript clearance is regulated and integrated into the gene expression regulation network for the establishment, maintenance, and exit from a special cellular state.
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Affiliation(s)
- Mingqiang Deng
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiwei Wang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China
| | - Peng Tang
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Peng Tang,
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21
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Huang Z, Peng Y, Wei Y, Tan Y. Nonsense-mediated mRNA decay promote C2C12 cell proliferation by targeting PIK3R5. J Muscle Res Cell Motil 2022; 44:11-23. [PMID: 36512272 DOI: 10.1007/s10974-022-09639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Nonsense mediated mRNA decay (NMD) is a highly conserved RNA quality control system, which can specifically clear abnormal mRNA and play an important role in tumorigenesis. Myoblast proliferation plays an important role in the repair of skeletal muscle injury and the development of myosarcoma, and is controlled by a variety of transcription factors and signals. The molecular mechanism by which NMD regulates the proliferation of myoblast cells is not completely clear. In this study, we found that the NMD activity of skeletal muscle is high in 1-week-old mice but decreases gradually with age, corresponding to a weakening capacity for muscle growth and regeneration. Here, we provide evidence that NMD plays an important role in myoblast proliferation and apoptosis. In addition, we found that PIK3R5 is an NMD substrate gene which can inhibit AKT activity and C2C12 cell proliferation. Therefore, NMD can target PIK3R5 to enhance AKT activity, which in turn promotes C2C12 cell proliferation. This study provides new insights into NMD regulatory mechanisms in muscular development and into potential novel therapeutic strategies for muscle atrophy.
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Affiliation(s)
- Zhenzhou Huang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Institute of Biomedical Sciences, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Yishu Peng
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Institute of Biomedical Sciences, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Yuhui Wei
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Institute of Biomedical Sciences, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Yanjie Tan
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Institute of Biomedical Sciences, Shandong Normal University, Jinan, 250014, Shandong, China.
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22
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Dose-related shifts in proteome and function of extracellular vesicles secreted by fetal neural stem cells following chronic alcohol exposure. Heliyon 2022; 8:e11348. [PMID: 36387439 PMCID: PMC9649983 DOI: 10.1016/j.heliyon.2022.e11348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/07/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence indicates that extracellular vesicles (EVs) mediate endocrine functions and also pathogenic effects of neurodevelopmental perturbagens like ethanol. We performed mass-spectrometry on EVs secreted by fetal murine cerebral cortical neural stem cells (NSCs), cultured ex-vivo as sex-specific neurosphere cultures, to identify overrepresented proteins and signaling pathways in EVs relative to parental NSCs in controls, and following exposure of parental NSCs to a dose range of ethanol. EV proteomes differ substantially from parental NSCs, and though EVs sequester proteins across sub-cellular compartments, they are enriched for distinct morphogenetic signals including the planar cell polarity pathway. Ethanol exposure favored selective protein sequestration in EVs and depletion in parental NSCs, and also resulted in dose-independent overrepresentation of cell-cycle and DNA replication pathways in EVs as well as dose-dependent overrepresentation of rRNA processing and mTor stress pathways. Transfer of untreated EVs to naïve cells resulted in decreased oxidative metabolism and S-phase, while EVs derived from ethanol-treated NSCs exhibited diminished effect. Collectively, these data show that NSCs secrete EVs with a distinct proteome that may have a general growth-inhibitory effect on recipient cells. Moreover, while ethanol results in selective transfer of proteins from NSCs to EVs, the efficacy of these exposure-derived EVs is diminished.
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23
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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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24
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Cho H, Abshire ET, Popp MW, Pröschel C, Schwartz JL, Yeo GW, Maquat LE. AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay. Mol Cell 2022; 82:2779-2796.e10. [PMID: 35675814 PMCID: PMC9357146 DOI: 10.1016/j.molcel.2022.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/21/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
Abstract
Despite a long appreciation for the role of nonsense-mediated mRNA decay (NMD) in destroying faulty, disease-causing mRNAs and maintaining normal, physiologic mRNA abundance, additional effectors that regulate NMD activity in mammalian cells continue to be identified. Here, we describe a haploid-cell genetic screen for NMD effectors that has unexpectedly identified 13 proteins constituting the AKT signaling pathway. We show that AKT supersedes UPF2 in exon-junction complexes (EJCs) that are devoid of RNPS1 but contain CASC3, defining an unanticipated insulin-stimulated EJC. Without altering UPF1 RNA binding or ATPase activity, AKT-mediated phosphorylation of the UPF1 CH domain at T151 augments UPF1 helicase activity, which is critical for NMD and also decreases the dependence of helicase activity on ATP. We demonstrate that upregulation of AKT signaling contributes to the hyperactivation of NMD that typifies Fragile X syndrome, as exemplified using FMR1-KO neural stem cells derived from induced pluripotent stem cells.
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Affiliation(s)
- Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Elizabeth T Abshire
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Stem Cell and Regenerative Medicine Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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25
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, 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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26
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No-nonsense: insights into the functional interplay of nonsense-mediated mRNA decay factors. Biochem J 2022; 479:973-993. [PMID: 35551602 PMCID: PMC9162471 DOI: 10.1042/bcj20210556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
Abstract
Nonsense-mediated messenger RNA decay (NMD) represents one of the main surveillance pathways used by eukaryotic cells to control the quality and abundance of mRNAs and to degrade viral RNA. NMD recognises mRNAs with a premature termination codon (PTC) and targets them to decay. Markers for a mRNA with a PTC, and thus NMD, are a long a 3′-untranslated region and the presence of an exon-junction complex (EJC) downstream of the stop codon. Here, we review our structural understanding of mammalian NMD factors and their functional interplay leading to a branched network of different interconnected but specialised mRNA decay pathways. We discuss recent insights into the potential impact of EJC composition on NMD pathway choice. We highlight the coexistence and function of different isoforms of up-frameshift protein 1 (UPF1) with an emphasis of their role at the endoplasmic reticulum and during stress, and the role of the paralogs UPF3B and UPF3A, underscoring that gene regulation by mammalian NMD is tightly controlled and context-dependent being conditional on developmental stage, tissue and cell types.
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27
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Wallmeroth D, Lackmann JW, Kueckelmann S, Altmüller J, Dieterich C, Boehm V, Gehring NH. Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay. EMBO J 2022; 41:e109191. [PMID: 35451084 PMCID: PMC9108619 DOI: 10.15252/embj.2021109191] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 12/14/2022] Open
Abstract
The paralogous human proteins UPF3A and UPF3B are involved in recognizing mRNAs targeted by nonsense‐mediated mRNA decay (NMD). UPF3B has been demonstrated to support NMD, presumably by bridging an exon junction complex (EJC) to the NMD factor UPF2. The role of UPF3A has been described either as a weak NMD activator or an NMD inhibitor. Here, we present a comprehensive functional analysis of UPF3A and UPF3B in human cells using combinatory experimental approaches. Overexpression or knockout of UPF3A as well as knockout of UPF3B did not substantially change global NMD activity. In contrast, the co‐depletion of UPF3A and UPF3B resulted in a marked NMD inhibition and a transcriptome‐wide upregulation of NMD substrates, demonstrating a functional redundancy between both NMD factors. In rescue experiments, UPF2 or EJC binding‐deficient UPF3B largely retained NMD activity. However, combinations of different mutants, including deletion of the middle domain, showed additive or synergistic effects and therefore failed to maintain NMD. Collectively, UPF3A and UPF3B emerge as fault‐tolerant, functionally redundant NMD activators in human cells.
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Affiliation(s)
- Damaris Wallmeroth
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Sabrina Kueckelmann
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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28
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Yi Z, Arvola RM, Myers S, Dilsavor CN, Abu Alhasan R, Carter BN, Patton RD, Bundschuh R, Singh G. Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding. EMBO J 2022; 41:e109202. [PMID: 35451102 PMCID: PMC9108626 DOI: 10.15252/embj.2021109202] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/30/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is governed by the three conserved factors-UPF1, UPF2, and UPF3. While all three are required for NMD in yeast, UPF3B is dispensable for NMD in mammals, and its paralog UPF3A is suggested to only weakly activate or even repress NMD due to its weaker binding to the exon junction complex (EJC). Here, we characterize the UPF3A/B-dependence of NMD in human cell lines deleted of one or both UPF3 paralogs. We show that in human colorectal cancer HCT116 cells, NMD can operate in a UPF3B-dependent and -independent manner. While UPF3A is almost dispensable for NMD in wild-type cells, it strongly activates NMD in cells lacking UPF3B. Notably, NMD remains partially active in cells lacking both UPF3 paralogs. Complementation studies in these cells show that EJC-binding domain of UPF3 paralogs is dispensable for NMD. Instead, the conserved "mid" domain of UPF3 paralogs is consequential for their NMD activity. Altogether, our results demonstrate that the mammalian UPF3 proteins play a more active role in NMD than simply bridging the EJC and the UPF complex.
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Affiliation(s)
- Zhongxia Yi
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - René M Arvola
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Sean Myers
- Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Corinne N Dilsavor
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Rabab Abu Alhasan
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Bayley N Carter
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Robert D Patton
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA.,Department of Chemistry and Biochemistry, The Ohio State University , Columbus, OH, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Guramrit Singh
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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29
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NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes Dev 2022; 36:348-367. [PMID: 35241478 PMCID: PMC8973849 DOI: 10.1101/gad.347690.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Here, Huth et al. investigated the role of components of the nonsense-mediated mRNA decay (NMD) pathway in regulating embryonic stem cell (ESC) differentiation, and show that NMD controls expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform (Eif4a2PTC). Their findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions. Cell fate transitions depend on balanced rewiring of transcription and translation programs to mediate ordered developmental progression. Components of the nonsense-mediated mRNA decay (NMD) pathway have been implicated in regulating embryonic stem cell (ESC) differentiation, but the exact mechanism is unclear. Here we show that NMD controls expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform (Eif4a2PTC). NMD deficiency leads to translation of the truncated eIF4A2PTC protein. eIF4A2PTC elicits increased mTORC1 activity and translation rates and causes differentiation delays. This establishes a previously unknown feedback loop between NMD and translation initiation. Furthermore, our results show a clear hierarchy in the severity of target deregulation and differentiation phenotypes between NMD effector KOs (Smg5 KO > Smg6 KO > Smg7 KO), which highlights heterodimer-independent functions for SMG5 and SMG7. Together, our findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions.
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30
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Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis. Cells 2021; 10:cells10123365. [PMID: 34943873 PMCID: PMC8699217 DOI: 10.3390/cells10123365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
SMG6 is an endonuclease, which cleaves mRNAs during nonsense-mediated mRNA decay (NMD), thereby regulating gene expression and controling mRNA quality. SMG6 has been shown as a differentiation license factor of totipotent embryonic stem cells. To investigate whether it controls the differentiation of lineage-specific pluripotent progenitor cells, we inactivated Smg6 in murine embryonic neural stem cells. Nestin-Cre-mediated deletion of Smg6 in mouse neuroprogenitor cells (NPCs) caused perinatal lethality. Mutant mice brains showed normal structure at E14.5 but great reduction of the cortical NPCs and late-born cortical neurons during later stages of neurogenesis (i.e., E18.5). Smg6 inactivation led to dramatic cell death in ganglionic eminence (GE) and a reduction of interneurons at E14.5. Interestingly, neurosphere assays showed self-renewal defects specifically in interneuron progenitors but not in cortical NPCs. RT-qPCR analysis revealed that the interneuron differentiation regulators Dlx1 and Dlx2 were reduced after Smg6 deletion. Intriguingly, when Smg6 was deleted specifically in cortical and hippocampal progenitors, the mutant mice were viable and showed normal size and architecture of the cortex at E18.5. Thus, SMG6 regulates cell fate in a cell type-specific manner and is more important for neuroprogenitors originating from the GE than for progenitors from the cortex.
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31
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Andjus S, Morillon A, Wery M. From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory. Noncoding RNA 2021; 7:ncrna7030044. [PMID: 34449682 PMCID: PMC8395947 DOI: 10.3390/ncrna7030044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022] Open
Abstract
The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes.
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Affiliation(s)
- Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France;
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
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32
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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33
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SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity. Nat Commun 2021; 12:3965. [PMID: 34172724 PMCID: PMC8233366 DOI: 10.1038/s41467-021-24046-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 05/30/2021] [Indexed: 12/28/2022] Open
Abstract
Eukaryotic gene expression is constantly controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation, resulting in phosphorylation of the central NMD factor UPF1 and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional connection between the final NMD steps. Transcriptome-wide analyses of SMG5-SMG7-depleted cells confirm exhaustive NMD inhibition resulting in massive transcriptomic alterations. Intriguingly, we find that the functionally underestimated SMG5 can substitute the role of SMG7 and individually activate NMD. Furthermore, the presence of either SMG5 or SMG7 is sufficient to support SMG6-mediated endonucleolysis of NMD targets. Our data support an improved model for NMD execution that features two-factor authentication involving UPF1 phosphorylation and SMG5-SMG7 recruitment to access SMG6 activity. Degradation of nonsense mediated mRNA decay (NMD) substrates is carried out by two seemingly independent pathways, SMG6-mediated endonucleolytic cleavage and/or SMG5-SMG7-induced accelerated deadenylation. Here the authors show that SMG5-SMG7 maintain NMD activity by permitting SMG6 activation.
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34
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Zhu X, Zhang H, Mendell JT. Ribosome Recycling by ABCE1 Links Lysosomal Function and Iron Homeostasis to 3' UTR-Directed Regulation and Nonsense-Mediated Decay. Cell Rep 2021; 32:107895. [PMID: 32668236 PMCID: PMC7433747 DOI: 10.1016/j.celrep.2020.107895] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/09/2020] [Accepted: 06/22/2020] [Indexed: 12/26/2022] Open
Abstract
Nonsense-mediated decay (NMD) is a pathway that degrades mRNAs containing premature termination codons. Here we describe a genome-wide screen for NMD factors that uncovers an unexpected mechanism that broadly governs 3' untranslated region (UTR)-directed regulation. The screen reveals that NMD requires lysosomal acidification, which allows transferrin-mediated iron uptake, which, in turn, is necessary for iron-sulfur (Fe-S) cluster biogenesis. This pathway maintains the activity of the Fe-S cluster-containing ribosome recycling factor ABCE1, whose impaired function results in movement of ribosomes into 3' UTRs, where they displace exon junction complexes, abrogating NMD. Importantly, these effects extend beyond NMD substrates, with ABCE1 activity required to maintain the accessibility of 3' UTRs to diverse regulators, including microRNAs and RNA binding proteins. Because of the sensitivity of the Fe-S cluster of ABCE1 to iron availability and reactive oxygen species, these findings reveal an unanticipated vulnerability of 3' UTR-directed regulation to lysosomal dysfunction, iron deficiency, and oxidative stress.
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Affiliation(s)
- Xiaoqiang Zhu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - He Zhang
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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35
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Nogueira G, Fernandes R, García-Moreno JF, Romão L. Nonsense-mediated RNA decay and its bipolar function in cancer. Mol Cancer 2021; 20:72. [PMID: 33926465 PMCID: PMC8082775 DOI: 10.1186/s12943-021-01364-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Nonsense-mediated decay (NMD) was first described as a quality-control mechanism that targets and rapidly degrades aberrant mRNAs carrying premature termination codons (PTCs). However, it was found that NMD also degrades a significant number of normal transcripts, thus arising as a mechanism of gene expression regulation. Based on these important functions, NMD regulates several biological processes and is involved in the pathophysiology of a plethora of human genetic diseases, including cancer. The present review aims to discuss the paradoxical, pro- and anti-tumorigenic roles of NMD, and how cancer cells have exploited both functions to potentiate the disease. Considering recent genetic and bioinformatic studies, we also provide a comprehensive overview of the present knowledge of the advantages and disadvantages of different NMD modulation-based approaches in cancer therapy, reflecting on the challenges imposed by the complexity of this disease. Furthermore, we discuss significant advances in the recent years providing new perspectives on the implications of aberrant NMD-escaping frameshifted transcripts in personalized immunotherapy design and predictive biomarker optimization. A better understanding of how NMD differentially impacts tumor cells according to their own genetic identity will certainly allow for the application of novel and more effective personalized treatments in the near future.
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Affiliation(s)
- Gonçalo Nogueira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Rafael Fernandes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Juan F García-Moreno
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal. .,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
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36
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Akiyama T, Suzuki T, Yamamoto T. RNA decay machinery safeguards immune cell development and immunological responses. Trends Immunol 2021; 42:447-460. [PMID: 33858774 DOI: 10.1016/j.it.2021.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/30/2022]
Abstract
mRNA decay systems control mRNA abundance by counterbalancing transcription. Several recent studies show that mRNA decay pathways are crucial to conventional T and B cell development in vertebrates, in addition to suppressing autoimmunity and excessive inflammatory responses. Selective mRNA degradation triggered by the CCR4-NOT deadenylase complex appears to be required in lymphocyte development, cell quiescence, V(D)J (variable-diversity-joining) recombination, and prevention of inappropriate apoptosis in mice. Moreover, a recent study suggests that mRNA decay may be involved in preventing human hyperinflammatory disease. These findings imply that mRNA decay pathways in humans and mice do not simply maintain mRNA homeostatic turnover but can also precisely regulate immune development and immunological responses by selectively targeting mRNAs.
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Affiliation(s)
- Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan.
| | - Toru Suzuki
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Tadashi Yamamoto
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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37
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Lee PJ, Yang S, Sun Y, Guo JU. Regulation of nonsense-mediated mRNA decay in neural development and disease. J Mol Cell Biol 2021; 13:269-281. [PMID: 33783512 PMCID: PMC8339359 DOI: 10.1093/jmcb/mjab022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 11/26/2022] Open
Abstract
Eukaryotes have evolved a variety of mRNA surveillance mechanisms to detect and degrade aberrant mRNAs with potential deleterious outcomes. Among them, nonsense-mediated mRNA decay (NMD) functions not only as a quality control mechanism targeting aberrant mRNAs containing a premature termination codon but also as a posttranscriptional gene regulation mechanism targeting numerous physiological mRNAs. Despite its well-characterized molecular basis, the regulatory scope and biological functions of NMD at an organismal level are incompletely understood. In humans, mutations in genes encoding core NMD factors cause specific developmental and neurological syndromes, suggesting a critical role of NMD in the central nervous system. Here, we review the accumulating biochemical and genetic evidence on the developmental regulation and physiological functions of NMD as well as an emerging role of NMD dysregulation in neurodegenerative diseases.
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Affiliation(s)
- Paul Jongseo Lee
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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38
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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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39
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Polaski JT, Udy DB, Escobar-Hoyos LF, Askan G, Leach SD, Ventura A, Kannan R, Bradley RK. The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma. eLife 2021; 10:e62209. [PMID: 33404013 PMCID: PMC7846273 DOI: 10.7554/elife.62209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic adenosquamous carcinoma (PASC) is an aggressive cancer whose mutational origins are poorly understood. An early study reported high-frequency somatic mutations affecting UPF1, a nonsense-mediated mRNA decay (NMD) factor, in PASC, but subsequent studies did not observe these lesions. The corresponding controversy about whether UPF1 mutations are important contributors to PASC has been exacerbated by a paucity of functional studies. Here, we modeled two UPF1 mutations in human and mouse cells to find no significant effects on pancreatic cancer growth, acquisition of adenosquamous features, UPF1 splicing, UPF1 protein, or NMD efficiency. We subsequently discovered that 45% of UPF1 mutations reportedly present in PASCs are identical to standing genetic variants in the human population, suggesting that they may be non-pathogenic inherited variants rather than pathogenic mutations. Our data suggest that UPF1 is not a common functional driver of PASC and motivate further attempts to understand the genetic origins of these malignancies.
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Affiliation(s)
- Jacob T Polaski
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology Graduate Program, University of WashingtonSeattleUnited States
| | - Luisa F Escobar-Hoyos
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of Pathology, Stony Brook UniversityNew YorkUnited States
- Yale University School of MedicineNew HavenUnited States
| | - Gokce Askan
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Steven D Leach
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of Surgery, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Dartmouth Norris Cotton Cancer CenterLebanonUnited States
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Ram Kannan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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40
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Chen B, Wang H, Li D, Lin X, Ma Z, Zeng Y. Up-frameshift Protein 1 Promotes Tumor Progression by Regulating Apoptosis and Epithelial-Mesenchymal Transition of Colorectal Cancer. Technol Cancer Res Treat 2021; 20:15330338211064438. [PMID: 34939866 PMCID: PMC8721398 DOI: 10.1177/15330338211064438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/26/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Recently, accumulating evidence confirmed that up-frameshift protein 1 (UPF1) was aberrantly expressed in various cancers. However, the molecular mechanism mediated by UPF1 underlying colorectal carcinogenesis remains unclear. Method: Immunohistochemistry (IHC) and quantitative real-time polymerase chain reaction analysis were used to determine the expression level of UPF1 in colorectal cancer (CRC) tissues. CCK-8, EdU, transwell assay, and flow cytometry were performed to investigate the biological significance of UPF1. Epithelial-mesenchymal transition (EMT) and apoptosis associated markers were detected by western blotting. Results: We found that UPF1 expression was upregulated in CRC tissues and cell lines. Clinical analysis revealed that high UPF1 expression was positively correlated with advanced stage, lymph node metastasis and shorter survival. Knockdown of UPF1 suppressed cell proliferation and cell cycle progression. Functionally, UPF1 promotes tumor metastasis by inducing epithelial to mesenchymal transition. Further investigations revealed that knockdown of UPF1 promoted apoptosis through triggering DNA damage. Conclusions: Taken together, this research revealed that UPF1 plays an oncogenic role in CRC via regulating EMT and apoptosis and may be a potential therapeutic target for CRC.
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Affiliation(s)
- Binlie Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
- Medical College, Shantou University, Shantou, Guangdong, People's Republic of China
| | - Huaiming Wang
- The First Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Danfeng Li
- The First Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Xiaosheng Lin
- The First Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Zhiyan Ma
- The First Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
- Medical College, Shantou University, Shantou, Guangdong, People's Republic of China
| | - Yongming Zeng
- The First Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
- Yongming Zeng, Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, 57 Changping Road, Shantou, 515041, People's Republic of China.
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41
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Alzahrani F, Kuwahara H, Long Y, Al-Owain M, Tohary M, AlSayed M, Mahnashi M, Fathi L, Alnemer M, Al-Hamed MH, Lemire G, Boycott KM, Hashem M, Han W, Al-Maawali A, Al Mahrizi F, Al-Thihli K, Gao X, Alkuraya FS. Recessive, Deleterious Variants in SMG8 Expand the Role of Nonsense-Mediated Decay in Developmental Disorders in Humans. Am J Hum Genet 2020; 107:1178-1185. [PMID: 33242396 DOI: 10.1016/j.ajhg.2020.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
We have previously described a heart-, eye-, and brain-malformation syndrome caused by homozygous loss-of-function variants in SMG9, which encodes a critical component of the nonsense-mediated decay (NMD) machinery. Here, we describe four consanguineous families with four different likely deleterious homozygous variants in SMG8, encoding a binding partner of SMG9. The observed phenotype greatly resembles that linked to SMG9 and comprises severe global developmental delay, microcephaly, facial dysmorphism, and variable congenital heart and eye malformations. RNA-seq analysis revealed a general increase in mRNA expression levels with significant overrepresentation of core NMD substrates. We also identified increased phosphorylation of UPF1, a key SMG1-dependent step in NMD, which most likely represents the loss of SMG8--mediated inhibition of SMG1 kinase activity. Our data show that SMG8 and SMG9 deficiency results in overlapping developmental disorders that most likely converge mechanistically on impaired NMD.
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42
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The Branched Nature of the Nonsense-Mediated mRNA Decay Pathway. Trends Genet 2020; 37:143-159. [PMID: 33008628 DOI: 10.1016/j.tig.2020.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved translation-coupled quality control mechanism in all eukaryotes that regulates the expression of a significant fraction of both the aberrant and normal transcriptomes. In vertebrates, NMD has become an essential process owing to expansion of the diversity of NMD-regulated transcripts, particularly during various developmental processes. Surprisingly, however, some core NMD factors that are essential for NMD in simpler organisms appear to be dispensable for vertebrate NMD. At the same time, numerous NMD enhancers and suppressors have been identified in multicellular organisms including vertebrates. Collectively, the available data suggest that vertebrate NMD is a complex, branched pathway wherein individual branches regulate specific mRNA subsets to fulfill distinct physiological functions.
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43
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Echols J, Siddiqui A, Dai Y, Havasi V, Sun R, Kaczmarczyk A, Keeling KM. A regulated NMD mouse model supports NMD inhibition as a viable therapeutic option to treat genetic diseases. Dis Model Mech 2020; 13:dmm044891. [PMID: 32737261 PMCID: PMC7473645 DOI: 10.1242/dmm.044891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/17/2020] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) targets mRNAs that contain a premature termination codon (PTC) for degradation, preventing their translation. By altering the expression of PTC-containing mRNAs, NMD modulates the inheritance pattern and severity of genetic diseases. NMD also limits the efficiency of suppressing translation termination at PTCs, an emerging therapeutic approach to treat genetic diseases caused by in-frame PTCs (nonsense mutations). Inhibiting NMD may help rescue partial levels of protein expression. However, it is unclear whether long-term, global NMD attenuation is safe. We hypothesize that a degree of NMD inhibition can be safely tolerated after completion of prenatal development. To test this hypothesis, we generated a novel transgenic mouse that expresses an inducible, dominant-negative form of human UPF1 (dnUPF1) to inhibit NMD in mouse tissues by different degrees, allowing us to examine the effects of global NMD inhibition in vivo A thorough characterization of these mice indicated that expressing dnUPF1 at levels that promote relatively moderate to strong NMD inhibition in most tissues for a 1-month period produced modest immunological and bone alterations. In contrast, 1 month of dnUPF1 expression to promote more modest NMD inhibition in most tissues did not produce any discernable defects, indicating that moderate global NMD attenuation is generally well tolerated in non-neurological somatic tissues. Importantly, a modest level of NMD inhibition that produced no overt abnormalities was able to significantly enhance in vivo PTC suppression. These results suggest that safe levels of NMD attenuation are likely achievable, and this can help rescue protein deficiencies resulting from PTCs.
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Affiliation(s)
- Josh Echols
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amna Siddiqui
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yanying Dai
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Viktoria Havasi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Richard Sun
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aneta Kaczmarczyk
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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44
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Sun Y, Eshov A, Zhou J, Isiktas AU, Guo JU. C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression. Nat Commun 2020; 11:3354. [PMID: 32620797 PMCID: PMC7335171 DOI: 10.1038/s41467-020-17129-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Expansion of an intronic (GGGGCC)n repeat region within the C9orf72 gene is a main cause of familial amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). A hallmark of c9ALS/FTD is the accumulation of misprocessed RNAs, which are often targets of cellular RNA surveillance. Here, we show that RNA decay mechanisms involving upstream frameshift 1 (UPF1), including nonsense-mediated decay (NMD), are inhibited in c9ALS/FTD brains and in cultured cells expressing either of two arginine-rich dipeptide repeats (R-DPRs), poly(GR) and poly(PR). Mechanistically, although R-DPRs cause the recruitment of UPF1 to stress granules, stress granule formation is independent of NMD inhibition. Instead, NMD inhibition is primarily a result from global translational repression caused by R-DPRs. Overexpression of UPF1, but none of its NMD-deficient mutants, enhanced the survival of neurons treated by R-DPRs, suggesting that R-DPRs cause neurotoxicity in part by inhibiting cellular RNA surveillance. C9orf72 repeat expansion is the major genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, the authors show that transcriptome aberrations commonly found in c9ALS/FTD are a result from defects in cellular RNA surveillance pathways that involve an RNA helicase UPF1.
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Affiliation(s)
- Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Aziz Eshov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jeffrey Zhou
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Atagun U Isiktas
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 06520, USA.
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45
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Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
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Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
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46
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The Complex Relationship between HTLV-1 and Nonsense-Mediated mRNA Decay (NMD). Pathogens 2020; 9:pathogens9040287. [PMID: 32326562 PMCID: PMC7238105 DOI: 10.3390/pathogens9040287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 02/07/2023] Open
Abstract
Before the establishment of an adaptive immune response, retroviruses can be targeted by several cellular host factors at different stages of the viral replication cycle. This intrinsic immunity relies on a large diversity of antiviral processes. In the case of HTLV-1 infection, these active innate host defense mechanisms are debated. Among these mechanisms, we focused on an RNA decay pathway called nonsense-mediated mRNA decay (NMD), which can target multiple viral RNAs, including HTLV-1 unspliced RNA, as has been recently demonstrated. NMD is a co-translational process that depends on the RNA helicase UPF1 and regulates the expression of multiple types of host mRNAs. RNA sensitivity to NMD depends on mRNA organization and the ribonucleoprotein (mRNP) composition. HTLV-1 has evolved several means to evade the NMD threat, leading to NMD inhibition. In the early steps of infection, NMD inhibition favours the production of HTLV-1 infectious particles, which may contribute to the survival of the fittest clones despite genome instability; however, its direct long-term impact remains to be investigated.
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47
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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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48
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Xing TR, Chen P, Wu JM, Gao LL, Yang W, Cheng Y, Tong LB. UPF1 Participates in the Progression of Endometrial Cancer by Inhibiting the Expression of lncRNA PVT1. Onco Targets Ther 2020; 13:2103-2114. [PMID: 32210576 PMCID: PMC7074825 DOI: 10.2147/ott.s233149] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Endometrial carcinoma (EC) is the primary cause of death associated with cancer globally. Thus, the possible molecular mechanism of EC needs further exploration. Up-frameshift protein 1 (UPF1) is an ATPase depending on RNA/DNA and RNA helicase depending on ATP. Long noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) was dysregulated in diverse diseases. METHODS qRT-PCR and Western blot were applied to detect UPF1 and PVT1 in EC. CCK-8, colony formation, and Transwell assays were used to test the effects of UPF1/PVT1 on cell proliferation and migration. Cells were cultured with actinomycin D to observe mRNA stability, and RNA immunoprecipitation assay was applied to verified the relationship between UPF1 and PVT1. Glucose consumption and lactate generation were measured when cells were transfected with siRNA. RESULTS Results demonstrated that the expression of UPF1 exhibited a remarkable decrement in EC tissues relative to that in non-tumor tissues. Subsequent functional experiments suggested that UPF1 decrement stimulated EC cells to grow and migrate. Moreover, UPF1 was discovered to be linked to PVT1 and had an inverse correlation with PVT1. Besides, PVT1 expression affected EC growth and migration, and PVT1 decrement alleviated the influence of UPF1 decrement on EC growth and migration and strengthened glycolysis in EC. CONCLUSION In this study, we found that UPF1 was down-regulated in EC tissues, and UPF1 might exert its role by regulating the expression of PVT1.
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Affiliation(s)
- Tian-rong Xing
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Ping Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Jia-mei Wu
- Department of Pathophysiology, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Li-li Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Wei Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Yu Cheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
| | - Li-bo Tong
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, People’s Republic of China
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49
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Kurosaki T, Popp MW, Maquat LE. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 2020; 20:406-420. [PMID: 30992545 DOI: 10.1038/s41580-019-0126-2] [Citation(s) in RCA: 421] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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50
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Broseus L, Ritchie W. Challenges in detecting and quantifying intron retention from next generation sequencing data. Comput Struct Biotechnol J 2020; 18:501-508. [PMID: 32206209 PMCID: PMC7078297 DOI: 10.1016/j.csbj.2020.02.010] [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: 09/03/2019] [Revised: 11/29/2019] [Accepted: 02/15/2020] [Indexed: 12/17/2022] Open
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computational assumptions that may lead to dramatically different results. We describe the various approaches for mitigating errors in detecting intron retention and for discovering IR signatures between different conditions.
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