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Lai S, Shiraishi H, Sebastian WA, Shimizu N, Umeda R, Ikeuchi M, Kiyota K, Takeno T, Miyazaki S, Yano S, Shimada T, Yoshimura A, Hanada R, Hanada T. Effect of nonsense-mediated mRNA decay factor SMG9 deficiency on premature aging in zebrafish. Commun Biol 2024; 7:654. [PMID: 38806677 PMCID: PMC11133409 DOI: 10.1038/s42003-024-06356-6] [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: 06/20/2023] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
SMG9 is an essential component of the nonsense-mediated mRNA decay (NMD) machinery, a quality control mechanism that selectively degrades aberrant transcripts. Mutations in SMG9 are associated with heart and brain malformation syndrome (HBMS). However, the molecular mechanism underlying HBMS remains unclear. We generated smg9 mutant zebrafish (smg9oi7/oi7) that have a lifespan of approximately 6 months or longer, allowing for analysis of the in vivo function of Smg9 in adults in more detail. smg9oi7/oi7 zebrafish display congenital brain abnormalities and reduced cardiac contraction. Additionally, smg9oi7/oi7 zebrafish exhibit a premature aging phenotype. Analysis of NMD target mRNAs shows a trend toward increased mRNA levels in smg9oi7/oi7 zebrafish. Spermidine oxidase (Smox) is increased in smg9oi7/oi7 zebrafish, resulting in the accumulation of byproducts, reactive oxygen species, and acrolein. The accumulation of smox mRNA due to NMD dysregulation caused by Smg9 deficiency leads to increased oxidative stress, resulting in premature aging.
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Affiliation(s)
- Shaohong Lai
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hiroshi Shiraishi
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | | | - Nobuyuki Shimizu
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Ryohei Umeda
- Department of Neurophysiology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Mayo Ikeuchi
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kyoko Kiyota
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Takashi Takeno
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Shuya Miyazaki
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Shinji Yano
- Institute for Research Management, Oita University, Yufu, Oita, Japan
| | - Tatsuo Shimada
- Oita Medical Technology School, Japan College of Judo-Therapy, Acupuncture & Moxibustion Therapy, Oita, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Reiko Hanada
- Department of Neurophysiology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Toshikatsu Hanada
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan.
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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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Zhang H, Peyton L, McCarroll A, de León Guerrerro SD, Zhang S, Gowda P, Sirkin D, El Achwah M, Duhe A, Wood WG, Jamison B, Tracy G, Pollak R, Hart RP, Pato CN, Mulle JG, Sanders AR, Pang ZP, Duan J. Scaled and Efficient Derivation of Loss of Function Alleles in Risk Genes for Neurodevelopmental and Psychiatric Disorders in Human iPSC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585542. [PMID: 38562852 PMCID: PMC10983959 DOI: 10.1101/2024.03.18.585542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Translating genetic findings for neurodevelopmental and psychiatric disorders (NPD) into actionable disease biology would benefit from large-scale and unbiased functional studies of NPD genes. Leveraging the cytosine base editing (CBE) system, here we developed a pipeline for clonal loss-of-function (LoF) allele mutagenesis in human induced pluripotent stem cells (hiPSCs) by introducing premature stop-codons (iSTOP) that lead to mRNA nonsense-mediated-decay (NMD) or protein truncation. We tested the pipeline for 23 NPD genes on 3 hiPSC lines and achieved highly reproducible, efficient iSTOP editing in 22 NPD genes. Using RNAseq, we confirmed their pluripotency, absence of chromosomal abnormalities, and NMD. Interestingly, for three schizophrenia risk genes (SETD1A, TRIO, CUL1), despite the high efficiency of base editing, we only obtained heterozygous LoF alleles, suggesting their essential roles for cell growth. We replicated the reported neural phenotypes of SHANK3-haploinsufficiency and found CUL1-LoF reduced neurite branches and synaptic puncta density. This iSTOP pipeline enables a scaled and efficient LoF mutagenesis of NPD genes, yielding an invaluable shareable resource.
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Affiliation(s)
- Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Lilia Peyton
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Ada McCarroll
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Sol Díaz de León Guerrerro
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
| | - Prarthana Gowda
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - David Sirkin
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Mahmoud El Achwah
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alexandra Duhe
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Whitney G Wood
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Brandon Jamison
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Gregory Tracy
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Rebecca Pollak
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University
| | - Carlos N Pato
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
| | - Jennifer G Mulle
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alan R Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
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4
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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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5
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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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6
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Zavileyskiy LG, Pervouchine DD. Post-transcriptional Regulation of Gene Expression via Unproductive Splicing. Acta Naturae 2024; 16:4-13. [PMID: 38698955 PMCID: PMC11062102 DOI: 10.32607/actanaturae.27337] [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: 12/03/2023] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
Unproductive splicing is a mechanism of post-transcriptional gene expression control in which premature stop codons are inserted into protein-coding transcripts as a result of regulated alternative splicing, leading to their degradation via the nonsense-mediated decay pathway. This mechanism is especially characteristic of RNA-binding proteins, which regulate each other's expression levels and those of other genes in multiple auto- and cross-regulatory loops. Deregulation of unproductive splicing is a cause of serious human diseases, including cancers, and is increasingly being considered as a prominent therapeutic target. This review discusses the types of unproductive splicing events, the mechanisms of auto- and cross-regulation, nonsense-mediated decay escape, and problems in identifying unproductive splice isoforms. It also provides examples of deregulation of unproductive splicing in human diseases and discusses therapeutic strategies for its correction using antisense oligonucleotides and small molecules.
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Affiliation(s)
- L. G. Zavileyskiy
- Lomonosov Moscow State University, Moscow, 119192 Russian Federation
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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7
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Patro I, Sahoo A, Nayak BR, Das R, Majumder S, Panigrahi GK. Nonsense-Mediated mRNA Decay: Mechanistic Insights and Physiological Significance. Mol Biotechnol 2023:10.1007/s12033-023-00927-4. [PMID: 37930508 DOI: 10.1007/s12033-023-00927-4] [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: 07/12/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation. It essentially ensures recognition and removal of aberrant transcripts. Therefore, the NMD protects the cellular system by restricting the synthesis of truncated proteins, potentially by eliminating the faulty mRNAs. NMD is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation as well. Primarily, the NMD machinery scans and differentiates the aberrant and non-aberrant transcripts. A myriad of cellular dysfunctions arise due to production of truncated proteins, so the NMD core proteins, the up-frameshift factors (UPFs) recognizes the faulty mRNAs and further recruits factors resulting in the mRNA degradation. NMD exhibits astounding variability in its ability in regulating cellular mechanisms including both pathological and physiological events. But, the detailed underlying molecular mechanisms in NMD remains blurred and require extensive investigation to gain insights on cellular homeostasis. The complexity in understanding of NMD pathway arises due to the involvement of numerous proteins, molecular interactions and their functioning in different steps of this process. Moreover methods such as alternative splicing generates numerous isoforms of mRNA, so it makes difficulties in understanding the impact of alternative splicing on the efficiency of NMD functioning. Role of NMD in cancer development is very complex. Studies have shown that in some cases cancer cells use NMD pathway as a tool to exploit the NMD mechanism to maintain tumor microenvironment. A greater level of understanding about the intricate mechanism of how tumor used NMD pathway for their benefits, a strategy can be developed for targeting and inhibiting NMD factors involved in pro-tumor activity. There are very little amount of information available about the NMD pathway, how it discriminate mRNAs that are targeted by NMD from those that are not. This review highlights our current understanding of NMD, specifically the regulatory mechanisms and attempts to outline less explored questions that warrant further investigations. Taken as a whole, a detailed molecular understanding of the NMD mechanism could lead to wide-ranging applications for improving cellular homeostasis and paving out strategies in combating pathological disorders leaping forward toward achieving United Nations sustainable development goals (SDG 3: Good health and well-being).
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Affiliation(s)
- Ipsita Patro
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Annapurna Sahoo
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
| | - Bilash Ranjan Nayak
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Rutupurna Das
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Sanjoy Majumder
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Gagan Kumar Panigrahi
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
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8
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Monaghan L, Longman D, Cáceres JF. Translation-coupled mRNA quality control mechanisms. EMBO J 2023; 42:e114378. [PMID: 37605642 PMCID: PMC10548175 DOI: 10.15252/embj.2023114378] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.
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Affiliation(s)
- Laura Monaghan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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9
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Shen S, Zhang C, Meng Y, Cui G, Wang Y, Liu X, He Q. Sensing of H2O2-induced oxidative stress by the UPF factor complex is crucial for activation of catalase-3 expression in Neurospora. PLoS Genet 2023; 19:e1010985. [PMID: 37844074 PMCID: PMC10578600 DOI: 10.1371/journal.pgen.1010985] [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: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
UPF-1-UPF-2-UPF-3 complex-orchestrated nonsense-mediated mRNA decay (NMD) is a well-characterized eukaryotic cellular surveillance mechanism that not only degrades aberrant transcripts to protect the integrity of the transcriptome but also eliminates normal transcripts to facilitate appropriate cellular responses to physiological and environmental changes. Here, we describe the multifaceted regulatory roles of the Neurospora crassa UPF complex in catalase-3 (cat-3) gene expression, which is essential for scavenging H2O2-induced oxidative stress. First, losing UPF proteins markedly slowed down the decay rate of cat-3 mRNA. Second, UPF proteins indirectly attenuated the transcriptional activity of cat-3 gene by boosting the decay of cpc-1 and ngf-1 mRNAs, which encode a well-studied transcription factor and a histone acetyltransferase, respectively. Further study showed that under oxidative stress condition, UPF proteins were degraded, followed by increased CPC-1 and NGF-1 activity, finally activating cat-3 expression to resist oxidative stress. Together, our data illustrate a sophisticated regulatory network of the cat-3 gene mediated by the UPF complex under physiological and H2O2-induced oxidative stress conditions.
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Affiliation(s)
- Shuangjie Shen
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chengcheng Zhang
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuanhao Meng
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guofei Cui
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Wang
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Qun He
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
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10
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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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Yang L, Wei J, Ma X, Cheng R, Zhang H, Jin T. Pan-Cancer Analysis of the Prognostic and Immunological Role of SMG5: A Biomarker for Cancers. Oncology 2023; 102:168-182. [PMID: 37699361 DOI: 10.1159/000533421] [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: 05/04/2023] [Accepted: 07/29/2023] [Indexed: 09/14/2023]
Abstract
INTRODUCTION SMG5 is involved in tumor cell development and viewed as a potential target for immunotherapy. The purpose of this study was to systematically analyze the expression level, function, and prognostic value of SMG5 in pan-cancers. METHODS Differential expression of SMG5 in normal and tumor tissues was analyzed using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Database (GTEx) data. Survival analysis was performed by Kaplan-Meier method and Cox risk regression. The relationship between SMG5 expression and lymphocyte abundance, tumor cell immune infiltration level, molecular and immune subtypes as well as immune checkpoints was analyzed by tumor-immune system interactions database (TISIDB), Tumor Immune Estimation Resource (TIMER), and Sangerbox databases. The correlation between SMG5 and immune scores was studied using the Estimation of Stromal and Immune Cells in Malignant Tumours using Expression (ESTIMATE) data algorithm. Further, drug sensitivity analysis of SMG5 with low-grade glioma (LGG) was conducted using the CellMiner database. RESULTS SMG5 was highly expressed in 23 tumors and only had a significant impact on the prognosis of patients with LGG only. In addition, in tumor microenvironment and tumor immune analysis, we found that the level of immune infiltration, tumor mutational load, microsatellite instability, and immune checkpoints of LGG were significantly correlated with SMG5 expression. Furthermore, SMG5 was significantly associated with immune scores, stromal scores, and sensitivity of some drugs in LGG. CONCLUSION SMG5 is differentially expressed in several cancers and is significantly associated with prognosis, immune microenvironment, and immune checkpoints in LGG patients. Therefore, SMG5 could be a potential pan-cancer biomarker and an immunotherapeutic target for LGG.
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Affiliation(s)
- Leteng Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Jie Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Xiaoya Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Rui Cheng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Huan Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
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12
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Nasif S, Colombo M, Uldry AC, Schröder M, de Brot S, Mühlemann O. Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells. NAR Cancer 2023; 5:zcad048. [PMID: 37681034 PMCID: PMC10480688 DOI: 10.1093/narcan/zcad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA decay pathway with roles in cellular stress responses, differentiation, and viral defense. It functions in both quality control and post-transcriptional regulation of gene expression. NMD has also emerged as a modulator of cancer progression, although available evidence supports both a tumor suppressor and a pro-tumorigenic role, depending on the model. To further investigate the role of NMD in cancer, we knocked out the NMD factor SMG7 in the HT1080 human fibrosarcoma cell line, resulting in suppression of NMD function. We then compared the oncogenic properties of the parental cell line, the SMG7-knockout, and a rescue cell line in which we re-introduced both isoforms of SMG7. We also tested the effect of a drug inhibiting the NMD factor SMG1 to distinguish NMD-dependent effects from putative NMD-independent functions of SMG7. Using cell-based assays and a mouse xenograft tumor model, we showed that suppression of NMD function severely compromises the oncogenic phenotype. Molecular pathway analysis revealed that NMD suppression strongly reduces matrix metalloprotease 9 (MMP9) expression and that MMP9 re-expression partially rescues the oncogenic phenotype. Since MMP9 promotes cancer cell migration and invasion, metastasis and angiogenesis, its downregulation may contribute to the reduced tumorigenicity of NMD-suppressed cells. Collectively, our results highlight the potential value of NMD inhibition as a therapeutic approach.
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Affiliation(s)
- Sofia Nasif
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
| | - Martino Colombo
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Switzerland
| | - Markus S Schröder
- NCCR RNA & Disease Bioinformatics Support,Department of Biology, ETH Zürich, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
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13
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Halbout M, Bury M, Hanet A, Gerin I, Graff J, Killian T, Gatto L, Vertommen D, Bommer GT. SUZ domain-containing proteins have multiple effects on nonsense-mediated decay target transcripts. J Biol Chem 2023; 299:105095. [PMID: 37507022 PMCID: PMC10470013 DOI: 10.1016/j.jbc.2023.105095] [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: 01/31/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Many transcripts are targeted by nonsense-mediated decay (NMD), leading to their degradation and the inhibition of their translation. We found that the protein SUZ domain-containing protein 1 (SZRD1) interacts with the key NMD factor up-frameshift 1. When recruited to NMD-sensitive reporter gene transcripts, SZRD1 increased protein production, at least in part, by relieving translational inhibition. The conserved SUZ domain in SZRD1 was required for this effect. The SUZ domain is present in only three other human proteins besides SZRD1: R3H domain-containing protein 1 and 2 (R3HDM1, R3HDM2) and cAMP-regulated phosphoprotein 21 (ARPP21). We found that ARPP21, similarly to SZRD1, can increase protein production from NMD-sensitive reporter transcripts in an SUZ domain-dependent manner. This indicated that the SUZ domain-containing proteins could prevent translational inhibition of transcripts targeted by NMD. Consistent with the idea that SZRD1 mainly prevents translational inhibition, we did not observe a systematic decrease in the abundance of NMD targets when we knocked down SZRD1. Surprisingly, knockdown of SZRD1 in two different cell lines led to reduced levels of the NMD component UPF3B, which was accompanied by increased levels in a subset of NMD targets. This suggests that SZRD1 is required to maintain normal UPF3B levels and indicates that the effect of SZRD1 on NMD targets is not limited to a relief from translational inhibition. Overall, our study reveals that human SUZ domain-containing proteins play a complex role in regulating protein output from transcripts targeted by NMD.
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Affiliation(s)
- Mathias Halbout
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Marina Bury
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Aoife Hanet
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Isabelle Gerin
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Julie Graff
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Theodore Killian
- Computational Biology Laboratory, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Laurent Gatto
- Computational Biology Laboratory, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Guido T Bommer
- Department of Physiological Chemistry, de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium.
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14
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Sun B, Chen L. Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues. Genome Biol 2023; 24:164. [PMID: 37434206 PMCID: PMC10337212 DOI: 10.1186/s13059-023-03004-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Nonsense-mediated mRNA decay (NMD) was originally conceived as an mRNA surveillance mechanism to prevent the production of potentially deleterious truncated proteins. Research also shows NMD is an important post-transcriptional gene regulation mechanism selectively targeting many non-aberrant mRNAs. However, how natural genetic variants affect NMD and modulate gene expression remains elusive. RESULTS Here we elucidate NMD regulation of individual genes across human tissues through genetical genomics. Genetic variants corresponding to NMD regulation are identified based on GTEx data through unique and robust transcript expression modeling. We identify genetic variants that influence the percentage of NMD-targeted transcripts (pNMD-QTLs), as well as genetic variants regulating the decay efficiency of NMD-targeted transcripts (dNMD-QTLs). Many such variants are missed in traditional expression quantitative trait locus (eQTL) mapping. NMD-QTLs show strong tissue specificity especially in the brain. They are more likely to overlap with disease single-nucleotide polymorphisms (SNPs). Compared to eQTLs, NMD-QTLs are more likely to be located within gene bodies and exons, especially the penultimate exons from the 3' end. Furthermore, NMD-QTLs are more likely to be found in the binding sites of miRNAs and RNA binding proteins. CONCLUSIONS We reveal the genome-wide landscape of genetic variants associated with NMD regulation across human tissues. Our analysis results indicate important roles of NMD in the brain. The preferential genomic positions of NMD-QTLs suggest key attributes for NMD regulation. Furthermore, the overlap with disease-associated SNPs and post-transcriptional regulatory elements implicates regulatory roles of NMD-QTLs in disease manifestation and their interactions with other post-transcriptional regulators.
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Affiliation(s)
- Bo Sun
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
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15
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Chen C, Shen Y, Li L, Ren Y, Wang ZQ, Li T. UPF3A is dispensable for nonsense-mediated mRNA decay in mouse pluripotent and somatic cells. Life Sci Alliance 2023; 6:e202201589. [PMID: 36997282 PMCID: PMC10070813 DOI: 10.26508/lsa.202201589] [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: 07/04/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/01/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved regulatory mechanism of post-transcriptional gene expression in eukaryotic cells. NMD plays essential roles in mRNA quality and quantity control and thus safeguards multiple biological processes including embryonic stem cell differentiation and organogenesis. UPF3A and UPF3B in vertebrate species, originated from a single UPF3 gene in yeast, are key factors in the NMD machinery. Although UPF3B is a well-recognized weak NMD-promoting factor, whether UPF3A functions in promoting or suppressing NMD is under debate. In this study, we generated a Upf3a conditional knockout mouse strain and established multiple lines of embryonic stem cells and somatic cells without UPF3A. Through extensive analysis on the expressions of 33 NMD targets, we found UPF3A neither represses NMD in mouse embryonic stem cells, somatic cells, nor in major organs including the liver, spleen, and thymus. Our study reinforces that UPF3A is dispensable for NMD when UPF3B is present. Furthermore, UPF3A may weakly and selectively promote NMD in certain murine organs.
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Affiliation(s)
- Chengyan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yanmin Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Luqian Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yaoxin Ren
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
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16
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Valcarce DG, Riesco MF, Cuesta-Martín L, Esteve-Codina A, Martínez-Vázquez JM, Robles V. Stress decreases spermatozoa quality and induces molecular alterations in zebrafish progeny. BMC Biol 2023; 21:70. [PMID: 37013516 PMCID: PMC10071778 DOI: 10.1186/s12915-023-01570-w] [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: 08/17/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Chronic stress can produce a severe negative impact on health not only in the exposed individuals but also in their offspring. Indeed, chronic stress may be contributing to the current worldwide scenario of increasing infertility and decreasing gamete quality in human populations. Here, we evaluate the effect of chronic stress on behavior and male reproductive parameters in zebrafish. Our goal is to provide information on the impact that chronic stress has at molecular, histological, and physiological level in a vertebrate model species. RESULTS We evaluated the effects of a 21-day chronic stress protocol covering around three full waves of spermatogenesis in Danio rerio adult males. The induction of chronic stress produced anxiety-like behavior in stressed males as assessed by a novel tank test. At a molecular level, the induction of chronic stress consistently resulted in the overexpression of two genes related to endoplasmic reticulum (ER) stress in the brain. Gene set enrichment analysis (GSEA) of testes suggested a dysregulation of the nonsense-mediated decay (NMD) pathway, which was also confirmed on qPCR analysis. Histological analysis of the testicle did not show significant differences in terms of the relative proportions of each germ-cell type; however, the quality of sperm from stressed males was compromised in terms of motility. RNA-seq analysis in stress-derived larval progenies revealed molecular alterations, including those predicted to affect translation initiation, DNA repair, cell cycle control, and response to stress. CONCLUSIONS Induction of chronic stress during a few cycles of spermatogenesis in the vertebrate zebrafish model affects behavior, gonadal gene expression, final gamete quality, and progeny. The NMD surveillance pathway (a key cellular mechanism that regulates the stability of both normal and mutant transcripts) is severely affected in the testes by chronic stress and therefore the control and regulation of RNAs during spermatogenesis may be affected altering the molecular status in the progeny.
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Affiliation(s)
- David G Valcarce
- Cell Biology Area, Molecular Biology Department, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
- Instituto Español de Oceanografía, Centro Oceanográfico de Santander (COST-IEO), CSIC, Calle Severiano Ballesteros 16. 39004, Santander, Spain
| | - Marta F Riesco
- Cell Biology Area, Molecular Biology Department, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Leyre Cuesta-Martín
- Cell Biology Area, Molecular Biology Department, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Juan Manuel Martínez-Vázquez
- Instituto Español de Oceanografía, Centro Oceanográfico de Santander (COST-IEO), CSIC, Calle Severiano Ballesteros 16. 39004, Santander, Spain
| | - Vanesa Robles
- Cell Biology Area, Molecular Biology Department, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain.
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17
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Elucidation of the Landscape of Alternatively Spliced Genes and Features in the Dorsal Striatum of Aggressive/Aggression-Deprived Mice in the Model of Chronic Social Conflicts. Genes (Basel) 2023; 14:genes14030599. [PMID: 36980872 PMCID: PMC10048575 DOI: 10.3390/genes14030599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Both aggressive and aggression-deprived (AD) individuals represent pathological cases extensively studied in psychiatry and substance abuse disciplines. We employed the animal model of chronic social conflicts curated in our laboratory for over 30 years. In the study, we pursued the task of evaluation of the key events in the dorsal striatum transcriptomes of aggression-experienced mice and AD species, as compared with the controls, using RNA-seq profiling. We evaluated the alternative splicing-mediated transcriptome dynamics based on the RNA-seq data. We confined our attention to the exon skipping (ES) events as the major AS type for animals. We report the concurrent posttranscriptional and posttranslational regulation of the ES events observed in the phosphorylation cycles (in phosphoproteins and their targets) in the neuron-specific genes of the striatum. Strikingly, we found that major neurospecific splicing factors (Nova1, Ptbp1, 2, Mbnl1, 2, and Sam68) related to the alternative splicing regulation of cAMP genes (Darpp-32, Grin1, Ptpn5, Ppp3ca, Pde10a, Prkaca, Psd95, and Adora1) are upregulated specifically in aggressive individuals as compared with the controls and specifically AD animals, assuming intense switching between isoforms in the cAMP-mediated (de)phosphorylation signaling cascade. We found that the coding alternative splicing events were mostly attributed to synaptic plasticity and neural development-related proteins, while the nonsense-mediated decay-associated splicing events are mostly attributed to the mRNA processing of genes, including the spliceosome and splicing factors. In addition, considering the gene families, the transporter (Slc) gene family manifested most of the ES events. We found out that the major molecular systems employing AS for their plasticity are the ‘spliceosome’, ‘chromatin rearrangement complex’, ‘synapse’, and ‘neural development/axonogenesis’ GO categories. Finally, we state that approximately 35% of the exon skipping variants in gene coding regions manifest the noncoding variants subject to nonsense-mediated decay, employed as a homeostasis-mediated expression regulation layer and often associated with the corresponding gene expression alteration.
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18
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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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19
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Palo A, Patel SA, Sahoo B, Chowdary TK, Dixit M. FRG1 is a direct transcriptional regulator of nonsense-mediated mRNA decay genes. Genomics 2023; 115:110539. [PMID: 36521634 DOI: 10.1016/j.ygeno.2022.110539] [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: 06/14/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
FRG1 is the primary candidate gene for Fascioscapulohumeral Muscular Dystrophy. So far, its role has been reported in muscle development, vasculogenesis, angiogenesis, and tumorigenesis. Mechanistically studies suggest FRG1's role in RNA biogenesis which may have implications in multiple physiological processes and diseases, including tumorigenesis. Its probable role as hnRNP and association with NMD-related genes prompted us to look into FRG1's effect on NMD gene expression and the mechanism. Using microarray profiling in cell lines, we found that FRG1 altered the mRNA surveillance pathway and associated pathways, such as RNA transport and spliceosome machinery molecules. Multiple sequence alignment of core factors, namely, UPF1, UPF3B, and SMG1, showed conserved stretches of nucleotide sequence 'CTGGG'. Structural modeling followed by EMSA, ChIP-qPCR, and luciferase reporter assays showed 'CTGGG' as a FRG1 binding site. Analysis of the publicly available datasets showed that the expression of FRG1 correlates with NMD genes in different tissue types. We validated the effect of FRG1 on NMD gene transcription by qRT-PCR. Overall, FRG1 might be a transcriptional regulator of NMD genes.
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Affiliation(s)
- Ananya Palo
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Saket Awadhesbhai Patel
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Bibekananda Sahoo
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Tirumala Kumar Chowdary
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Manjusha Dixit
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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20
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Chapman JH, Craig JM, Wang CD, Gundlach JH, Neuman K, Hogg J. UPF1 mutants with intact ATPase but deficient helicase activities promote efficient nonsense-mediated mRNA decay. Nucleic Acids Res 2022; 50:11876-11894. [PMID: 36370101 PMCID: PMC9723629 DOI: 10.1093/nar/gkac1026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/12/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
The conserved RNA helicase UPF1 coordinates nonsense-mediated mRNA decay (NMD) by engaging with mRNAs, RNA decay machinery and the terminating ribosome. UPF1 ATPase activity is implicated in mRNA target discrimination and completion of decay, but the mechanisms through which UPF1 enzymatic activities such as helicase, translocase, RNP remodeling, and ATPase-stimulated dissociation influence NMD remain poorly defined. Using high-throughput biochemical assays to quantify UPF1 enzymatic activities, we show that UPF1 is only moderately processive (<200 nt) in physiological contexts and undergoes ATPase-stimulated dissociation from RNA. We combine an in silico screen with these assays to identify and characterize known and novel UPF1 mutants with altered helicase, ATPase, and RNA binding properties. We find that UPF1 mutants with substantially impaired processivity (E797R, G619K/A546H), faster (G619K) or slower (K547P, E797R, G619K/A546H) unwinding rates, and/or reduced mechanochemical coupling (i.e. the ability to harness ATP hydrolysis for work; K547P, R549S, G619K, G619K/A546H) can still support efficient NMD of well-characterized targets in human cells. These data are consistent with a central role for UPF1 ATPase activity in driving cycles of RNA binding and dissociation to ensure accurate NMD target selection.
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Affiliation(s)
- Joseph H Chapman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Clara D Wang
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Robert Hogg
- To whom correspondence should be addressed. Tel: +1 301 827 0724; Fax: +1 301 451 5459;
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21
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Lehtiniemi T, Bourgery M, Ma L, Ahmedani A, Mäkelä M, Asteljoki J, Olotu O, Laasanen S, Zhang FP, Tan K, Chousal JN, Burow D, Koskinen S, Laiho A, Elo L, Chalmel F, Wilkinson M, Kotaja N. SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis. Nucleic Acids Res 2022; 50:11470-11491. [PMID: 36259644 PMCID: PMC9723633 DOI: 10.1093/nar/gkac900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 12/24/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA turnover pathway that depends on the endonuclease SMG6. Here, we show that SMG6 is essential for male germ cell differentiation in mice. Germ-cell conditional knockout (cKO) of Smg6 induces extensive transcriptome misregulation, including a failure to eliminate meiotically expressed transcripts in early haploid cells, and accumulation of NMD target mRNAs with long 3' untranslated regions (UTRs). Loss of SMG6 in the male germline results in complete arrest of spermatogenesis at the early haploid cell stage. We find that SMG6 is strikingly enriched in the chromatoid body (CB), a specialized cytoplasmic granule in male germ cells also harboring PIWI-interacting RNAs (piRNAs) and the piRNA-binding protein PIWIL1. This raises the possibility that SMG6 and the piRNA pathway function together, which is supported by several findings, including that Piwil1-KO mice phenocopy Smg6-cKO mice and that SMG6 and PIWIL1 co-regulate many genes in round spermatids. Together, our results demonstrate that SMG6 is an essential regulator of the male germline transcriptome, and highlight the CB as a molecular platform coordinating RNA regulatory pathways to control sperm production and fertility.
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Affiliation(s)
- Tiina Lehtiniemi
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Matthieu Bourgery
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Lin Ma
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Ammar Ahmedani
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Margareeta Mäkelä
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Juho Asteljoki
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Opeyemi Olotu
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Samuli Laasanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Fu-Ping Zhang
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Turku Center for Disease Modeling, University of Turku, Turku, Finland
- GM-Unit, Helsinki Institute of Life Science, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Dana Burow
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Satu Koskinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Frédéric Chalmel
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine (IGM), University of California, San Diego, La Jolla, CA 92093, USA
| | - Noora Kotaja
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
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22
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Llorca-Cardenosa MJ, Aronson LI, Krastev DB, Nieminuszczy J, Alexander J, Song F, Dylewska M, Broderick R, Brough R, Zimmermann A, Zenke FT, Gurel B, Riisnaes R, Ferreira A, Roumeliotis T, Choudhary J, Pettitt SJ, de Bono J, Cervantes A, Haider S, Niedzwiedz W, Lord CJ, Chong IY. SMG8/SMG9 Heterodimer Loss Modulates SMG1 Kinase to Drive ATR Inhibitor Resistance. Cancer Res 2022; 82:3962-3973. [PMID: 36273494 PMCID: PMC9627126 DOI: 10.1158/0008-5472.can-21-4339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/19/2022] [Accepted: 08/26/2022] [Indexed: 01/07/2023]
Abstract
Gastric cancer represents the third leading cause of global cancer mortality and an area of unmet clinical need. Drugs that target the DNA damage response, including ATR inhibitors (ATRi), have been proposed as novel targeted agents in gastric cancer. Here, we sought to evaluate the efficacy of ATRi in preclinical models of gastric cancer and to understand how ATRi resistance might emerge as a means to identify predictors of ATRi response. A positive selection genome-wide CRISPR-Cas9 screen identified candidate regulators of ATRi resistance in gastric cancer. Loss-of-function mutations in either SMG8 or SMG9 caused ATRi resistance by an SMG1-mediated mechanism. Although ATRi still impaired ATR/CHK1 signaling in SMG8/9-defective cells, other characteristic responses to ATRi exposure were not seen, such as changes in ATM/CHK2, γH2AX, phospho-RPA, or 53BP1 status or changes in the proportions of cells in S- or G2-M-phases of the cell cycle. Transcription/replication conflicts (TRC) elicited by ATRi exposure are a likely cause of ATRi sensitivity, and SMG8/9-defective cells exhibited a reduced level of ATRi-induced TRCs, which could contribute to ATRi resistance. These observations suggest ATRi elicits antitumor efficacy in gastric cancer but that drug resistance could emerge via alterations in the SMG8/9/1 pathway. SIGNIFICANCE These findings reveal how cancer cells acquire resistance to ATRi and identify pathways that could be targeted to enhance the overall effectiveness of these inhibitors.
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Affiliation(s)
| | | | - Dragomir B. Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - John Alexander
- The Institute of Cancer Research, London, United Kingdom
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | | | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Astrid Zimmermann
- The healthcare business of Merck KGaA, Biopharma R&D, Translational Innovation Platform Oncology, Darmstadt, Germany
| | - Frank T. Zenke
- The healthcare business of Merck KGaA, Biopharma R&D, Translational Innovation Platform Oncology, Darmstadt, Germany
| | - Bora Gurel
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Ruth Riisnaes
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Ana Ferreira
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Johann de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Andres Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, 46010, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Syed Haider
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Christopher J. Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Irene Y. Chong
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
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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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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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25
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The G3BP1-UPF1-Associated Long Non-Coding RNA CALA Regulates RNA Turnover in the Cytoplasm. Noncoding RNA 2022; 8:ncrna8040049. [PMID: 35893232 PMCID: PMC9326601 DOI: 10.3390/ncrna8040049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
Besides transcription, RNA decay accounts for a large proportion of regulated gene expression and is paramount for cellular functions. Classical RNA surveillance pathways, like nonsense-mediated decay (NMD), are also implicated in the turnover of non-mutant transcripts. Whereas numerous protein factors have been assigned to distinct RNA decay pathways, the contribution of long non-coding RNAs (lncRNAs) to RNA turnover remains unknown. Here we identify the lncRNA CALA as a potent regulator of RNA turnover in endothelial cells. We demonstrate that CALA forms cytoplasmic ribonucleoprotein complexes with G3BP1 and regulates endothelial cell functions. A detailed characterization of these G3BP1-positive complexes by mass spectrometry identifies UPF1 and numerous other NMD factors having cytoplasmic G3BP1-association that is CALA-dependent. Importantly, CALA silencing impairs degradation of NMD target transcripts, establishing CALA as a non-coding regulator of RNA steady-state levels in the endothelium.
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26
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Johnson MA, Nuckols TA, Merino P, Bagchi P, Nandy S, Root J, Taylor G, Seyfried NT, Kukar T. Proximity-based labeling reveals DNA damage-induced phosphorylation of fused in sarcoma (FUS) causes distinct changes in the FUS protein interactome. J Biol Chem 2022; 298:102135. [PMID: 35709984 PMCID: PMC9372748 DOI: 10.1016/j.jbc.2022.102135] [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: 10/05/2021] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 01/18/2023] Open
Abstract
Accumulation of cytoplasmic inclusions containing fused in sarcoma (FUS), an RNA/DNA-binding protein, is a common hallmark of frontotemporal lobar degeneration and amyotrophic lateral sclerosis neuropathology. We have previously shown that DNA damage can trigger the cytoplasmic accumulation of N-terminally phosphorylated FUS. However, the functional consequences of N-terminal FUS phosphorylation are unknown. To gain insight into this question, we utilized proximity-dependent biotin labeling via ascorbate peroxidase 2 aired with mass spectrometry to investigate whether N-terminal phosphorylation alters the FUS protein-protein interaction network (interactome), and subsequently, FUS function. We report the first analysis comparing the interactomes of three FUS variants: homeostatic wildtype FUS (FUS WT), phosphomimetic FUS (FUS PM; a proxy for N-terminally phosphorylated FUS), and the toxic FUS proline 525 to leucine mutant (FUS P525L) that causes juvenile amyotrophic lateral sclerosis. We found that the phosphomimetic FUS interactome is uniquely enriched for a group of cytoplasmic proteins that mediate mRNA metabolism and translation, as well as nuclear proteins involved in the spliceosome and DNA repair functions. Furthermore, we identified and validated the RNA-induced silencing complex RNA helicase MOV10 as a novel interacting partner of FUS. Finally, we provide functional evidence that N-terminally phosphorylated FUS may disrupt homeostatic translation and steady-state levels of specific mRNA transcripts. Taken together, these results highlight phosphorylation as a unique modulator of the interactome and function of FUS.
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Affiliation(s)
- Michelle A. Johnson
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Thomas A. Nuckols
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Paola Merino
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Srijita Nandy
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Jessica Root
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Georgia Taylor
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Nicholas T. Seyfried
- Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA,Emory Integrated Proteomics Core, Emory University, School of Medicine, Atlanta, Georgia, USA,Department of Neurology, Emory University, School of Medicine, Atlanta, Georgia, USA,Department of Biochemistry, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta, Georgia, USA,Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta, Georgia, USA,Department of Neurology, Emory University, School of Medicine, Atlanta, Georgia, USA,For correspondence: Thomas Kukar
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27
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Jefri M, Zhang X, Stumpf PS, Zhang L, Peng H, Hettige N, Theroux JF, Aouabed Z, Wilson K, Deshmukh S, Antonyan L, Ni A, Alsuwaidi S, Zhang Y, Jabado N, Garcia BA, Schuppert A, Bjornsson HT, Ernst C. Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4). Hum Mol Genet 2022; 31:3715-3728. [PMID: 35640156 PMCID: PMC9616574 DOI: 10.1093/hmg/ddac121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
Kabuki syndrome is frequently caused by loss-of-function mutations in one allele of histone 3 lysine 4 (H3K4) methyltransferase KMT2D and is associated with problems in neurological, immunological and skeletal system development. We generated heterozygous KMT2D knockout and Kabuki patient-derived cell models to investigate the role of reduced dosage of KMT2D in stem cells. We discovered chromosomal locus-specific alterations in gene expression, specifically a 110 Kb region containing Synaptotagmin 3 (SYT3), C-Type Lectin Domain Containing 11A (CLEC11A), Chromosome 19 Open Reading Frame 81 (C19ORF81) and SH3 And Multiple Ankyrin Repeat Domains 1 (SHANK1), suggesting locus-specific targeting of KMT2D. Using whole genome histone methylation mapping, we confirmed locus-specific changes in H3K4 methylation patterning coincident with regional decreases in gene expression in Kabuki cell models. Significantly reduced H3K4 peaks aligned with regions of stem cell maps of H3K27 and H3K4 methylation suggesting KMT2D haploinsufficiency impact bivalent enhancers in stem cells. Preparing the genome for subsequent differentiation cues may be of significant importance for Kabuki-related genes. This work provides a new insight into the mechanism of action of an important gene in bone and brain development and may increase our understanding of a specific function of a human disease-relevant H3K4 methyltransferase family member.
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Affiliation(s)
- Malvin Jefri
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Patrick S Stumpf
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen 52056, Germany
| | - Li Zhang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Huashan Peng
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Khadija Wilson
- Department of Biochemistry and Molecular, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Shriya Deshmukh
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Anjie Ni
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Shaima Alsuwaidi
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Ying Zhang
- Psychiatric Genetics Group, McGill University, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Verdun, Montreal, QC H4H 1R3, Canada,Department of Psychiatry, McGill University and Douglas Hospital Research Institute, Montreal, QC H4H 1R3, Canada
| | - Nada Jabado
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada,Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada,Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Andreas Schuppert
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen 52056, Germany
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Genetics and Molecular Medicine, Landspitali University Hospital, 101 Reykjavik, Iceland
| | - Carl Ernst
- To whom correspondence should be addressed at: Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle boulevard, Frank Common building, Room 2101.2 Verdun, QC H4H 1R3, Canada. Tel: +1 514-761-6131 ext 3382; Fax: +1 514-762-3023;
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28
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Fritz SE, Ranganathan S, Wang CD, Hogg JR. An alternative UPF1 isoform drives conditional remodeling of nonsense-mediated mRNA decay. EMBO J 2022; 41:e108898. [PMID: 35403729 PMCID: PMC9108617 DOI: 10.15252/embj.2021108898] [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: 06/07/2021] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway monitors translation termination in order to degrade transcripts with premature stop codons and regulate thousands of human genes. Here, we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1LL , enables condition-dependent remodeling of NMD specificity. Previous studies indicate that the extension of a conserved regulatory loop in the UPF1LL helicase core confers a decreased propensity to dissociate from RNA upon ATP hydrolysis relative to UPF1SL , the major UPF1 isoform. Using biochemical and transcriptome-wide approaches, we find that UPF1LL can circumvent the protective RNA binding proteins PTBP1 and hnRNP L to preferentially bind and down-regulate transcripts with long 3'UTRs normally shielded from NMD. Unexpectedly, UPF1LL supports induction of NMD on new populations of substrate mRNAs in response to activation of the integrated stress response and impaired translation efficiency. Thus, while canonical NMD is abolished by moderate translational repression, UPF1LL activity is enhanced, offering the possibility to rapidly rewire NMD specificity in response to cellular stress.
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Affiliation(s)
- Sarah E Fritz
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - Soumya Ranganathan
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - Clara D Wang
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - J Robert Hogg
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
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29
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Sanderlin EJ, Keenan MM, Mense M, Revenko AS, Monia BP, Guo S, Huang L. CFTR mRNAs with nonsense codons are degraded by the SMG6-mediated endonucleolytic decay pathway. Nat Commun 2022; 13:2344. [PMID: 35487895 PMCID: PMC9054838 DOI: 10.1038/s41467-022-29935-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/24/2022] [Indexed: 12/22/2022] Open
Abstract
Approximately 10% of cystic fibrosis patients harbor nonsense mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene which can generate nonsense codons in the CFTR mRNA and subsequently activate the nonsense-mediated decay (NMD) pathway resulting in rapid mRNA degradation. However, it is not known which NMD branches govern the decay of CFTR mRNAs containing nonsense codons. Here we utilize antisense oligonucleotides targeting NMD factors to evaluate the regulation of nonsense codon-containing CFTR mRNAs by the NMD pathway. We observe that CFTR mRNAs with nonsense codons G542X, R1162X, and W1282X, but not Y122X, require UPF2 and UPF3 for NMD. Furthermore, we demonstrate that all evaluated CFTR mRNAs harboring nonsense codons are degraded by the SMG6-mediated endonucleolytic pathway rather than the SMG5-SMG7-mediated exonucleolytic pathway. Finally, we show that upregulation of all evaluated CFTR mRNAs with nonsense codons by NMD pathway inhibition improves outcomes of translational readthrough therapy.
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Affiliation(s)
| | | | - Martin Mense
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | | | | | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Lulu Huang
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA.
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30
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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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31
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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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32
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Lejeune F. Nonsense-Mediated mRNA Decay, a Finely Regulated Mechanism. Biomedicines 2022; 10:biomedicines10010141. [PMID: 35052820 PMCID: PMC8773229 DOI: 10.3390/biomedicines10010141] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a mechanism for rapidly eliminating mRNAs carrying a premature termination codon and a pathway that regulates many genes. This implies that NMD must be subject to regulation in order to allow, under certain physiological conditions, the expression of genes that are normally repressed by NMD. Therapeutically, it might be interesting to express certain NMD-repressed genes or to allow the synthesis of functional truncated proteins. Developing such approaches will require a good understanding of NMD regulation. This review describes the different levels of this regulation in human cells.
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Affiliation(s)
- Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France;
- Unité Tumorigenèse et Résistance aux Traitements, Institut Pasteur de Lille, F-59000 Lille, France
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33
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Abstract
Nonsense-mediated mRNA decay (NMD) is an mRNA degradation pathway that eliminates transcripts containing premature termination codons (PTCs). Half-lives of the mRNAs containing PTCs demonstrate that a small percent escape surveillance and do not degrade. It is not known whether this escape represents variable mRNA degradation within cells or, alternatively cells within the population are resistant. Here we demonstrate a single-cell approach with a bi-directional reporter, which expresses two β-globin genes with or without a PTC in the same cell, to characterize the efficiency of NMD in individual cells. We found a broad range of NMD efficiency in the population; some cells degraded essentially all of the mRNAs, while others escaped NMD almost completely. Characterization of NMD efficiency together with NMD regulators in single cells showed cell-to-cell variability of NMD reflects the differential level of surveillance factors, SMG1 and phosphorylated UPF1. A single-cell fluorescent reporter system that enabled detection of NMD using flow cytometry revealed that this escape occurred either by translational readthrough at the PTC or by a failure of mRNA degradation after successful translation termination at the PTC.
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34
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Mocciaro E, Runfola V, Ghezzi P, Pannese M, Gabellini D. DUX4 Role in Normal Physiology and in FSHD Muscular Dystrophy. Cells 2021; 10:3322. [PMID: 34943834 PMCID: PMC8699294 DOI: 10.3390/cells10123322] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/10/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
In the last decade, the sequence-specific transcription factor double homeobox 4 (DUX4) has gone from being an obscure entity to being a key factor in important physiological and pathological processes. We now know that expression of DUX4 is highly regulated and restricted to the early steps of embryonic development, where DUX4 is involved in transcriptional activation of the zygotic genome. While DUX4 is epigenetically silenced in most somatic tissues of healthy humans, its aberrant reactivation is associated with several diseases, including cancer, viral infection and facioscapulohumeral muscular dystrophy (FSHD). DUX4 is also translocated, giving rise to chimeric oncogenic proteins at the basis of sarcoma and leukemia forms. Hence, understanding how DUX4 is regulated and performs its activity could provide relevant information, not only to further our knowledge of human embryonic development regulation, but also to develop therapeutic approaches for the diseases associated with DUX4. Here, we summarize current knowledge on the cellular and molecular processes regulated by DUX4 with a special emphasis on FSHD muscular dystrophy.
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Affiliation(s)
| | | | | | | | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy; (E.M.); (V.R.); (P.G.); (M.P.)
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35
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Zinshteyn B, Sinha NK, Enam SU, Koleske B, Green R. Translational repression of NMD targets by GIGYF2 and EIF4E2. PLoS Genet 2021; 17:e1009813. [PMID: 34665823 PMCID: PMC8555832 DOI: 10.1371/journal.pgen.1009813] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/29/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Translation of messenger RNAs (mRNAs) with premature termination codons produces truncated proteins with potentially deleterious effects. This is prevented by nonsense-mediated mRNA decay (NMD) of these mRNAs. NMD is triggered by ribosomes terminating upstream of a splice site marked by an exon-junction complex (EJC), but also acts on many mRNAs lacking a splice junction after their termination codon. We developed a genome-wide CRISPR flow cytometry screen to identify regulators of mRNAs with premature termination codons in K562 cells. This screen recovered essentially all core NMD factors and suggested a role for EJC factors in degradation of PTCs without downstream splicing. Among the strongest hits were the translational repressors GIGYF2 and EIF4E2. GIGYF2 and EIF4E2 mediate translational repression but not mRNA decay of a subset of NMD targets and interact with NMD factors genetically and physically. Our results suggest a model wherein recognition of a stop codon as premature can lead to its translational repression through GIGYF2 and EIF4E2.
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Affiliation(s)
- Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Niladri K. Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Syed Usman Enam
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Benjamin Koleske
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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36
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Teran NA, Nachun DC, Eulalio T, Ferraro NM, Smail C, Rivas MA, Montgomery SB. Nonsense-mediated decay is highly stable across individuals and tissues. Am J Hum Genet 2021; 108:1401-1408. [PMID: 34216550 DOI: 10.1016/j.ajhg.2021.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022] Open
Abstract
Precise interpretation of the effects of rare protein-truncating variants (PTVs) is important for accurate determination of variant impact. Current methods for assessing the ability of PTVs to induce nonsense-mediated decay (NMD) focus primarily on the position of the variant in the transcript. We used RNA sequencing of the Genotype Tissue Expression v.8 cohort to compute the efficiency of NMD using allelic imbalance for 2,320 rare (genome aggregation database minor allele frequency ≤ 1%) PTVs across 809 individuals in 49 tissues. We created an interpretable predictive model using penalized logistic regression in order to evaluate the comprehensive influence of variant annotation, tissue, and inter-individual variation on NMD. We found that variant position, allele frequency, the inclusion of ultra-rare and singleton variants, and conservation were predictive of allelic imbalance. Furthermore, we found that NMD effects were highly concordant across tissues and individuals. Due to this high consistency, we demonstrate in silico that utilizing peripheral tissues or cell lines provides accurate prediction of NMD for PTVs.
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37
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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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38
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Cheruiyot A, Li S, Nonavinkere Srivatsan S, Ahmed T, Chen Y, Lemacon DS, Li Y, Yang Z, Wadugu BA, Warner WA, Pruett-Miller SM, Obeng EA, Link DC, He D, Xiao F, Wang X, Bailis JM, Walter MJ, You Z. Nonsense-Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells Harboring SF3B1 or U2AF1 Mutations. Cancer Res 2021; 81:4499-4513. [PMID: 34215620 DOI: 10.1158/0008-5472.can-20-4016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTC) for degradation, however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system to accurately measure NMD activity in individual cells. A genome-wide CRISPR-Cas9 knockout screen using this reporter system identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, cells with mutations in the spliceosome genes SF3B1 and U2AF1, which are commonly found in myelodysplastic syndrome (MDS) and cancers, have overall attenuated NMD activity. Compared with wild-type (WT) cells, SF3B1- and U2AF1-mutant cells were more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage, and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition was rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, these findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel synthetic lethal strategy for the treatment of MDS and cancers with spliceosome mutations. SIGNIFICANCE: This study has developed a novel NMD reporter system and identified a potential therapeutic approach of targeting the NMD pathway to treat cancer with spliceosome gene mutations.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Shan Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Sridhar Nonavinkere Srivatsan
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Tanzir Ahmed
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Yuhao Chen
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Delphine S Lemacon
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ying Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Zheng Yang
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Brian A Wadugu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Wayne A Warner
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Esther A Obeng
- Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel C Link
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Dalin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Fei Xiao
- Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiaowei Wang
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | | | - Matthew J Walter
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Zhongsheng You
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.
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39
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Baradaran-Heravi A, Balgi AD, Hosseini-Farahabadi S, Choi K, Has C, Roberge M. Effect of small molecule eRF3 degraders on premature termination codon readthrough. Nucleic Acids Res 2021; 49:3692-3708. [PMID: 33764477 PMCID: PMC8053119 DOI: 10.1093/nar/gkab194] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Premature termination codon (PTC) readthrough is considered a potential treatment for genetic diseases caused by nonsense mutations. High concentrations of aminoglycosides induce low levels of PTC readthrough but also elicit severe toxicity. Identifying compounds that enhance PTC readthrough by aminoglycosides or reduce their toxicity is a continuing challenge. In humans, a binary complex of eukaryotic release factors 1 (eRF1) and 3 (eRF3a or eRF3b) mediates translation termination. They also participate in the SURF (SMG1-UPF1-eRF1-eRF3) complex assembly involved in nonsense-mediated mRNA decay (NMD). We show that PTC readthrough by aminoglycoside G418 is considerably enhanced by eRF3a and eRF3b siRNAs and cereblon E3 ligase modulators CC-885 and CC-90009, which induce proteasomal degradation of eRF3a and eRF3b. eRF3 degradation also reduces eRF1 levels and upregulates UPF1 and selectively stabilizes TP53 transcripts bearing a nonsense mutation over WT, indicating NMD suppression. CC-90009 is considerably less toxic than CC-885 and it enhances PTC readthrough in combination with aminoglycosides in mucopolysaccharidosis type I-Hurler, late infantile neuronal ceroid lipofuscinosis, Duchenne muscular dystrophy and junctional epidermolysis bullosa patient-derived cells with nonsense mutations in the IDUA, TPP1, DMD and COL17A1 genes, respectively. Combination of CC-90009 with aminoglycosides such as gentamicin or ELX-02 may have potential for PTC readthrough therapy.
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Affiliation(s)
- Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Aruna D Balgi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sara Hosseini-Farahabadi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kunho Choi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cristina Has
- Department of Dermatology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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40
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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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41
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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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42
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Loss of the fragile X syndrome protein FMRP results in misregulation of nonsense-mediated mRNA decay. Nat Cell Biol 2021; 23:40-48. [PMID: 33420492 PMCID: PMC8273690 DOI: 10.1038/s41556-020-00618-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/29/2020] [Indexed: 01/28/2023]
Abstract
Loss of the fragile X protein FMRP is a leading cause of intellectual disability and autism1,2, but the underlying mechanism remains poorly understood. We report that FMRP deficiency results in hyperactivated nonsense-mediated mRNA decay (NMD)3,4 in human SH-SY5Y neuroblastoma cells and fragile X syndrome (FXS) fibroblast-derived induced pluripotent stem cells (iPSCs). We examined the underlying mechanism and found that the key NMD factor UPF1 binds directly to FMRP, promoting FMRP binding to NMD targets. Our data indicate that FMRP acts as an NMD repressor. In the absence of FMRP, NMD targets are relieved from FMRP-mediated translational repression so that their half-lives are decreased and, for those NMD targets encoding NMD factors, increased translation produces abnormally high factor levels despite their hyperactivated NMD. Transcriptome-wide alterations caused by NMD hyperactivation have a role in the FXS phenotype. Consistent with this, small-molecule-mediated inhibition of hyperactivated NMD, which typifies iPSCs derived from patients with FXS, restores a number of neurodifferentiation markers, including those not deriving from NMD targets. Our mechanistic studies reveal that many molecular abnormalities in FMRP-deficient cells are attributable-either directly or indirectly-to misregulated NMD.
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43
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UPF2 leads to degradation of dendritically targeted mRNAs to regulate synaptic plasticity and cognitive function. Mol Psychiatry 2020; 25:3360-3379. [PMID: 31636381 PMCID: PMC7566522 DOI: 10.1038/s41380-019-0547-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
Synaptic plasticity requires a tight control of mRNA levels in dendrites. RNA translation and degradation pathways have been recently linked to neurodevelopmental and neuropsychiatric diseases, suggesting a role for RNA regulation in synaptic plasticity and cognition. While the local translation of specific mRNAs has been implicated in synaptic plasticity, the tightly controlled mechanisms that regulate local quantity of specific mRNAs remain poorly understood. Despite being the only RNA regulatory pathway that is associated with multiple mental illnesses, the nonsense-mediated mRNA decay (NMD) pathway presents an unexplored regulatory mechanism for synaptic function and plasticity. Here, we show that neuron-specific disruption of UPF2, an NMD component, in adulthood attenuates learning, memory, spine density, synaptic plasticity (L-LTP), and potentiates perseverative/repetitive behavior in mice. We report that the NMD pathway operates within dendrites to regulate Glutamate Receptor 1 (GLUR1) surface levels. Specifically, UPF2 modulates the internalization of GLUR1 and promotes its local synthesis in dendrites. We identified neuronal Prkag3 mRNA as a mechanistic substrate for NMD that contributes to the UPF2-mediated regulation of GLUR1 by limiting total GLUR1 levels. These data establish that UPF2 regulates synaptic plasticity, cognition, and local protein synthesis in dendrites, providing fundamental insight into the neuron-specific function of NMD within the brain.
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Kontarakis Z, Stainier DY. Genetics in Light of Transcriptional Adaptation. Trends Genet 2020; 36:926-935. [DOI: 10.1016/j.tig.2020.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/04/2020] [Accepted: 08/14/2020] [Indexed: 11/27/2022]
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CELF2 regulates the species-specific alternative splicing of TREM2. Sci Rep 2020; 10:17995. [PMID: 33093587 PMCID: PMC7582162 DOI: 10.1038/s41598-020-75057-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/12/2020] [Indexed: 11/08/2022] Open
Abstract
Genetic variations of TREM2 have been implicated as a risk factor of Alzheimer’s disease (AD). Recent studies suggest that the loss of TREM2 function compromises microglial responses to the accumulation of amyloid beta. Previously, we found that exon 3 of TREM2 is an alternative exon whose skipping leads to a reduction in full-length TREM2 protein by inducing nonsense-mediated mRNA decay. Here, we aimed to identify factors regulating TREM2 splicing. Using a panel of RNA-binding proteins, we found that exon 3 skipping of TREM2 was promoted by two paralogous proteins, CELF1 and CELF2, which were both linked previously with risk loci of AD. Although the overexpression of both CELF1 and CELF2 enhanced exon 3 skipping, only CELF2 reduced the expression of full-length TREM2 protein. Notably, the TREM2 ortholog in the green monkey, but not in the mouse, showed alternative splicing of exon 3 like human TREM2. Similarly, splicing regulation of exon 3 by CELF1/2 was found to be common to humans and monkeys. Using chimeric minigenes of human and mouse TREM2, we mapped a CELF-responsive sequence within intron 3 of human TREM2. Collectively, our results revealed a novel regulatory factor of TREM2 expression and highlighted a species-dependent difference of its regulation.
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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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Domingo D, Nawaz U, Corbett M, Espinoza JL, Tatton-Brown K, Coman D, Wilkinson MF, Gecz J, Jolly LA. A synonymous UPF3B variant causing a speech disorder implicates NMD as a regulator of neurodevelopmental disorder gene networks. Hum Mol Genet 2020; 29:2568-2578. [PMID: 32667670 PMCID: PMC10893962 DOI: 10.1093/hmg/ddaa151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/22/2020] [Accepted: 07/11/2020] [Indexed: 11/12/2022] Open
Abstract
Loss-of-function mutations of the X-chromosome gene UPF3B cause male neurodevelopmental disorders (NDDs) via largely unknown mechanisms. We investigated initially by interrogating a novel synonymous UPF3B variant in a male with absent speech. In silico and functional studies using cell lines derived from this individual show altered UPF3B RNA splicing. The resulting mRNA species encodes a frame-shifted protein with a premature termination codon (PTC) predicted to elicit degradation via nonsense-mediated mRNA decay (NMD). UPF3B mRNA was reduced in the cell line, and no UPF3B protein was produced, confirming a loss-of-function allele. UPF3B is itself involved in the NMD mechanism which degrades both PTC-bearing mutant transcripts and also many physiological transcripts. RNAseq analysis showed that ~1.6% of mRNAs exhibited altered expression. These mRNA changes overlapped and correlated with those we identified in additional cell lines obtained from individuals harbouring other UPF3B mutations, permitting us to interrogate pathogenic mechanisms of UPF3B-associated NDDs. We identified 102 genes consistently deregulated across all UPF3B mutant cell lines. Of the 51 upregulated genes, 75% contained an NMD-targeting feature, thus identifying high-confidence direct NMD targets. Intriguingly, 22 of the dysregulated genes encoded known NDD genes, suggesting UPF3B-dependent NMD regulates gene networks critical for cognition and behaviour. Indeed, we show that 78.5% of all NDD genes encode a transcript predicted to be targeted by NMD. These data describe the first synonymous UPF3B mutation in a patient with prominent speech and language disabilities and identify plausible mechanisms of pathology downstream of UPF3B mutations involving the deregulation of NDD-gene networks.
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Affiliation(s)
- Deepti Domingo
- University of Adelaide and Robinson Research Institute, Adelaide, SA 5005, Australia
| | - Urwah Nawaz
- University of Adelaide and Robinson Research Institute, Adelaide, SA 5005, Australia
| | - Mark Corbett
- University of Adelaide and Robinson Research Institute, Adelaide, SA 5005, Australia
| | | | - Katrina Tatton-Brown
- St George’s University of London, London SW17, UK
- Southwest Thames Regional Genetics Centre, St George’s Healthcare NHS Trust, London SW17, UK
| | - David Coman
- School of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Miles F Wilkinson
- Department of Reproductive Medicine, 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
| | - Jozef Gecz
- University of Adelaide and Robinson Research Institute, Adelaide, SA 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- University of Adelaide and Robinson Research Institute, Adelaide, SA 5005, Australia
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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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Tan K, Jones SH, Lake BB, Chousal JN, Shum EY, Zhang L, Chen S, Sohni A, Pandya S, Gallo RL, Zhang K, Cook-Andersen H, Wilkinson MF. The role of the NMD factor UPF3B in olfactory sensory neurons. eLife 2020; 9:e57525. [PMID: 32773035 PMCID: PMC7452722 DOI: 10.7554/elife.57525] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Samantha H Jones
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Blue B Lake
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Eleen Y Shum
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Lingjuan Zhang
- Department of Dermatology, University of California, San DiegoSan DiegoUnited States
| | - Song Chen
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Shivam Pandya
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Richard L Gallo
- Department of Dermatology, University of California, San DiegoSan DiegoUnited States
| | - Kun Zhang
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
- Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
- Institute of Genomic Medicine, University of California, San DiegoSan DiegoUnited States
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50
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Longman D, Jackson-Jones KA, Maslon MM, Murphy LC, Young RS, Stoddart JJ, Hug N, Taylor MS, Papadopoulos DK, Cáceres JF. Identification of a localized nonsense-mediated decay pathway at the endoplasmic reticulum. Genes Dev 2020; 34:1075-1088. [PMID: 32616520 PMCID: PMC7397857 DOI: 10.1101/gad.338061.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022]
Abstract
Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the endoplasmic reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Furthermore, we show that NBAS fulfills an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 coregulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER-protective function by ensuring quality control of ER-translated mRNAs.
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Affiliation(s)
- Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Kathryn A Jackson-Jones
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robert S Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jack J Stoddart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Martin S Taylor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Dimitrios K Papadopoulos
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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