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Chen Y, Xia L, Peng Y, Wang G, Bi L, Xiao X, Li C, Li W. Corrigendum: Development and validation of a m 6A -regulated prognostic signature in lung adenocarcinoma. Front Oncol 2023; 13:1309950. [PMID: 38023249 PMCID: PMC10660251 DOI: 10.3389/fonc.2023.1309950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fonc.2022.947808.].
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Affiliation(s)
- Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuxuan Peng
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Wang
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liyun Bi
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xue Xiao
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cui Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, China
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2
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Hung MH, Chang CW, Wang KC, Chaisaingmongkol J, Ruchirawat M, Greten TF, Wang XW. Purine anabolism creates therapeutic vulnerability in hepatocellular carcinoma through m 6 A-mediated epitranscriptomic regulation. Hepatology 2023; 78:1462-1477. [PMID: 37094826 PMCID: PMC10593095 DOI: 10.1097/hep.0000000000000420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND AND AIMS Purines are building blocks for the cellular genome, and excessive purine nucleotides are seen in tumors. However, how purine metabolism is dysregulated in tumors, and impacting tumorigenesis remains elusive. APPROACH AND RESULTS Transcriptomic and metabolomic analyses of purine biosynthesis and purine degradation pathways were performed in the tumor and associated nontumor liver tissues obtained from 62 patients with HCC, one of the most lethal cancers worldwide. We found that most genes in purine synthesis are upregulated, while genes in purine degradation are inhibited in HCC tumors. High purine anabolism is associated with unique somatic mutational signatures linked to patient prognosis. Mechanistically, we discover that increasing purine anabolism promotes epitranscriptomic dysregulation of DNA damage repairing (DDR) machinery through upregulating RNA N6-methyladenosine (m 6 A) modification. High purine anabolic HCC is sensitive to DDR-targeting agents but not to standard HCC treatments, correlating with the clinical outcomes in 5 independent HCC cohorts containing 724 patients. We further showed that high purine anabolism determines the sensitivity to DDR-targeting agents in 5 HCC cell lines in vitro and in vivo . CONCLUSIONS Our results reveal a central role of purine anabolism in regulating DDR, which could be therapeutically exploited in HCC.
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Affiliation(s)
- Man Hsin Hung
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ching Wen Chang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kathy Cheng Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jittiporn Chaisaingmongkol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Thailand
| | - Mathuros Ruchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Thailand
| | - Tim F. Greten
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Lead contact
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3
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Madugalle SU, Liau WS, Zhao Q, Li X, Gong H, Marshall PR, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove MRB, Davies JWA, Kim G, Rauch S, He C, Dickinson BC, Fulopova B, Fletcher LN, Williams SR, Spitale RC, Bredy TW. Synapse-Enriched m 6A-Modified Malat1 Interacts with the Novel m 6A Reader, DPYSL2, and Is Required for Fear-Extinction Memory. J Neurosci 2023; 43:7084-7100. [PMID: 37669863 PMCID: PMC10601377 DOI: 10.1523/jneurosci.0943-23.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
The RNA modification N6-methyladenosine (m6A) regulates the interaction between RNA and various RNA binding proteins within the nucleus and other subcellular compartments and has recently been shown to be involved in experience-dependent plasticity, learning, and memory. Using m6A RNA-sequencing, we have discovered a distinct population of learning-related m6A- modified RNAs at the synapse, which includes the long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (Malat1). RNA immunoprecipitation and mass spectrometry revealed 12 new synapse-specific learning-induced m6A readers in the mPFC of male C57/BL6 mice, with m6A-modified Malat1 binding to a subset of these, including CYFIP2 and DPYSL2. In addition, a cell type- and synapse-specific, and state-dependent, reduction of m6A on Malat1 impairs fear-extinction memory; an effect that likely occurs through a disruption in the interaction between Malat1 and DPYSL2 and an associated decrease in dendritic spine formation. These findings highlight the critical role of m6A in regulating the functional state of RNA during the consolidation of fear-extinction memory, and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.SIGNIFICANCE STATEMENT We have discovered that learning-induced m6A-modified RNA (including the long noncoding RNA, Malat1) accumulates in the synaptic compartment. We have identified several new m6A readers that are associated with fear extinction learning and demonstrate a causal relationship between m6A-modified Malat1 and the formation of fear-extinction memory. These findings highlight the role of m6A in regulating the functional state of an RNA during memory formation and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.
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Affiliation(s)
| | - Wei-Siang Liau
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China 430071
- Medical Research Institute, Wuhan University, Wuhan, China 430014
| | - Hao Gong
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Paul R Marshall
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Ambika Periyakaruppiah
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Esmi L Zajaczkowski
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Laura J Leighton
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Haobin Ren
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Mason R B Musgrove
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Joshua W A Davies
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Gwangmin Kim
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Simone Rauch
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Bryan C Dickinson
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Barbora Fulopova
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Lee N Fletcher
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Stephen R Williams
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697
| | - Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
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Huang H, Song R, Wong JJ, Anggono V, Widagdo J. The N6-methyladenosine RNA landscape in the aged mouse hippocampus. Aging Cell 2022; 22:e13755. [PMID: 36495001 PMCID: PMC9835576 DOI: 10.1111/acel.13755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/13/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
The aged brain is associated with an inevitable decline in cognitive function and increased vulnerability to neurodegenerative disorders. Multiple molecular hallmarks have been associated with the aging nervous system through transcriptomics and proteomic studies. Recently, epitranscriptomic analysis has highlighted the role of RNA chemical modification in various biological processes. In particular, N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNAs, has been functionally linked to multiple aspects of RNA metabolism with the roles of m6A in processes such as learning and memory, leading to our current investigation of how the m6A-transcriptomic landscape is shaped during aging. Using the inbred C57BL/6 line, we compared the m6A-transcriptomic profiles from the hippocampi of young (3-month-old) and aged (20-month-old) mice. Methylated RNA immunoprecipitation (MeRIP)-sequencing analysis revealed hyper- and hypomethylation in 426 and 102 genes, respectively, in the aged hippocampus (fold change >1.5, false discovery rate <0.05). By correlating the methylation changes to their steady-state transcript levels in the RNA-Seq data, we found a significant concordance between m6A and transcript levels in both directions. Notably, the myelin regulator gene Gpr17 was downregulated in the aged hippocampus concomitant with reduced m6A levels in its 3'UTR. Using reporter constructs and mutagenesis analysis, we demonstrated that the putative m6A sites in the 3'UTR of Gpr17 are important for mRNA translation but not for regulating transcript stability. Overall, the positive correlation between m6A and the transcript expression levels indicates a co-transcriptional regulation of m6A with gene expression changes that occur in the aged mouse hippocampus.
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Affiliation(s)
- He Huang
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain Institute, The University of QueenslandBrisbaneQueenslandAustralia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary InstituteThe University of SydneyCamperdownNew South WalesAustralia,The University of SydneyFaculty of Medicine and HealthCamperdownNew South WalesAustralia
| | - Justin J.‐L. Wong
- Epigenetics and RNA Biology Program Centenary InstituteThe University of SydneyCamperdownNew South WalesAustralia,The University of SydneyFaculty of Medicine and HealthCamperdownNew South WalesAustralia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain Institute, The University of QueenslandBrisbaneQueenslandAustralia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain Institute, The University of QueenslandBrisbaneQueenslandAustralia
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Chen Y, Xia L, Peng Y, Wang G, Bi L, Xiao X, Li C, Li W. Development and validation of a m 6A -regulated prognostic signature in lung adenocarcinoma. Front Oncol 2022; 12:947808. [PMID: 36303829 PMCID: PMC9593055 DOI: 10.3389/fonc.2022.947808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most frequent subtype of lung cancer, with a 5-year survival rate of less than 20%. N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification in eukaryotic cells, and post-transcriptionally regulates gene expression and function by affecting RNA metabolism. The alterations of functionally important m6A sites have been previously shown to play vital roles in tumor initiation and progression, but little is known about the extent to which m6A-regulated genes play in prognostic performance for patients with LUAD. Here, we presented an overview of the m6A methylome in LUAD tissues using transcriptome-wide m6A methylation profiles, and found that differentially methylated transcripts were significantly enriched in tumor-related processes, including immune response, angiogenesis and cell-substrate adhesion. Joint analysis of m6A modification and gene expression suggested that 300 genes were regulated by m6A. Furthermore, we developed a m6A-regulated prognosis-associated signature (m6A-PPS) by performing a multi-step process. The m6A-PPS model, a 15-gene set, was qualified for prognosis prediction for LUAD patients. By regrouping the patients with this model, the OS of the high-risk group was shorter than that of the low-risk group across all datasets. Importantly, patients with high m6A-PPS scores respond better to immunotherapeutic. Our results provide a valuable resource for understanding the important role of epitranscriptomic modifications in the pathogenesis of LUAD, and obtain potential prognostic biomarkers.
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Affiliation(s)
- Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuxuan Peng
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Wang
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liyun Bi
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xue Xiao
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cui Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, China
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6
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Jousma J, Han Z, Yan G, Nukala SB, Kwon Y, Thi Le HH, Li Y, Ong SB, Lee WH, Ong SG. Alteration of the N 6-methyladenosine epitranscriptomic profile in synthetic phthalate-treated human induced pluripotent stem cell-derived endothelial cells. Epigenomics 2022; 14:1139-1155. [PMID: 36314267 PMCID: PMC9710528 DOI: 10.2217/epi-2022-0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Background: This study aimed to characterize the N6-methyladenosine epitranscriptomic profile induced by mono(2-ethylhexyl) phthalate (MEHP) exposure using a human-induced pluripotent stem cell-derived endothelial cell model. Methods: A multiomic approach was employed by performing RNA sequencing in parallel with an N6-methyladenosine-specific microarray to identify mRNAs, lncRNAs, and miRNAs affected by MEHP exposure. Results: An integrative multiomic analysis identified relevant biological features affected by MEHP, while functional assays provided a phenotypic characterization of these effects. Transcripts regulated by the epitranscriptome were validated with quantitative PCR and methylated RNA immunoprecipitation. Conclusion: The authors' profiling of the epitranscriptome expands the scope of toxicological insights into known environmental toxins to under surveyed cellular contexts and emerging domains of regulation and is, therefore, a valuable resource to human health.
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Affiliation(s)
- Jordan Jousma
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Zhenbo Han
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Gege Yan
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Sarath Babu Nukala
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Youjeong Kwon
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Hoai Huong Thi Le
- Department of Basic Medical Sciences, University of Arizona College of Medicine, ABC-1 Building, 425 North 5th Street, Phoenix, AZ 85004, USA
| | - Ya Li
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Sang-Bing Ong
- Department of Medicine & Therapeutics, Faculty of Medicine, Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- Centre for Cardiovascular Genomics & Medicine (CCGM), Lui Che Woo Institute of Innovative Medicine, CUHK, Hong Kong SAR, China
- Hong Kong Hub of Paediatric Excellence (HK HOPE), Hong Kong Children's Hospital (HKCH), Kowloon Bay, Hong Kong SAR, China
- Kunming Institute of Zoology – The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources & Molecular Research of Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Won Hee Lee
- Department of Basic Medical Sciences, University of Arizona College of Medicine, ABC-1 Building, 425 North 5th Street, Phoenix, AZ 85004, USA
| | - Sang-Ging Ong
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
- Department of Medicine & Therapeutics, Faculty of Medicine, Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
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Alvarado-Marchena L, Martínez-Pérez M, Aparicio F, Pallas V, Maumus F. Recent Acquisition of Functional m6A RNA Demethylase Domain in Orchid Ty3/Gypsy Elements. Front Plant Sci 2022; 13:939843. [PMID: 35860540 PMCID: PMC9289625 DOI: 10.3389/fpls.2022.939843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Long terminal repeats (LTR) retrotransposons are transposable elements (TEs) representing major components of most plant genomes. The fixation of additional conserved protein domains in their genomes is considered a rare event in the course of their evolution. Such changes can bring novel functions and increase their fitness by playing a role in the regulation of their replicative cycle or by affecting their integration landscape so that the detection of new domains can in turn reveal important aspects of host-TE interactions. We have mined angiosperm genomes for the presence of additional domains in LTR retrotransposons. We report a lineage of large (25 kbp) Gypsy-type elements in the genomes of Phalaenopsis orchids that contain an additional open reading frame containing a 2-ODD domain with close similarity to those responsible for m6A RNA demethylase activity in AlkB proteins. By performing in vitro assays, we demonstrate the RNA binding capability and the demethylase activity of the Gypsy-encoded AlkB protein, suggesting it could be functional against cognate TE mRNA or any cellular RNA in planta. In line with recent literature, we propose that the fixation of an RNA demethylase in this lineage of LTR retrotransposons may reflect an important role for epitranscriptomic control in host surveillance against TEs.
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Affiliation(s)
- Luis Alvarado-Marchena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Mireya Martínez-Pérez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Ingeniero Fausto Elio, Spain
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, Versailles, France
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Hammam E, Sinha A, Baumgarten S, Nardella F, Liang J, Miled S, Bonhomme F, Erdmann D, Arcangioli B, Arimondo PB, Dedon P, Preiser P, Scherf A. Malaria Parasite Stress Tolerance Is Regulated by DNMT2-Mediated tRNA Cytosine Methylation. mBio 2021;:e0255821. [PMID: 34724812 DOI: 10.1128/mBio.02558-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Malaria parasites need to cope with changing environmental conditions that require strong countermeasures to ensure pathogen survival in the human and mosquito hosts. The molecular mechanisms that protect Plasmodium falciparum homeostasis during the complex life cycle remain unknown. Here, we identify cytosine methylation of tRNAAsp (GTC) as being critical to maintain stable protein synthesis. Using conditional knockout (KO) of a member of the DNA methyltransferase family, called Pf-DNMT2, RNA bisulfite sequencing demonstrated the selective cytosine methylation of this enzyme of tRNAAsp (GTC) at position C38. Although no growth defect on parasite proliferation was observed, Pf-DNMT2KO parasites showed a selective downregulation of proteins with a GAC codon bias. This resulted in a significant shift in parasite metabolism, priming KO parasites for being more sensitive to various types of stress. Importantly, nutritional stress made tRNAAsp (GTC) sensitive to cleavage by an unknown nuclease and increased gametocyte production (>6-fold). Our study uncovers an epitranscriptomic mechanism that safeguards protein translation and homeostasis of sexual commitment in malaria parasites. IMPORTANCE P. falciparum is the most virulent malaria parasite species, accounting for the majority of the disease mortality and morbidity. Understanding how this pathogen is able to adapt to different cellular and environmental stressors during its complex life cycle is crucial in order to develop new strategies to tackle the disease. In this study, we identified the writer of a specific tRNA cytosine methylation site as a new layer of epitranscriptomic regulation in malaria parasites that regulates the translation of a subset of parasite proteins (>400) involved in different metabolic pathways. Our findings give insight into a novel molecular mechanism that regulates P. falciparum response to drug treatment and sexual commitment.
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9
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Zhang DY, Ming GL, Song H. PUS7: a targetable epitranscriptomic regulator of glioblastoma growth. Trends Pharmacol Sci 2021; 42:976-978. [PMID: 34657723 DOI: 10.1016/j.tips.2021.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Pseudouridine is the most abundant yet unexplored RNA modification in glioblastoma. Cui and coworkers find that PUS7, a pseudouridine depositing enzyme, promotes tumor growth and can be targeted by small molecule inhibitors. Mechanistically, PUS7 modifies tRNAs, reduces TYK2 translation, and downregulates a proliferation-restricting interferon-STAT1 pathway in glioblastoma.
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Affiliation(s)
- Daniel Y Zhang
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA; Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA; Glioblastoma Translational Center of Excellence, The Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA.
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10
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Farhat DC, Bowler MW, Communie G, Pontier D, Belmudes L, Mas C, Corrao C, Couté Y, Bougdour A, Lagrange T, Hakimi MA, Swale C. A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma. eLife 2021; 10:68312. [PMID: 34263725 PMCID: PMC8313237 DOI: 10.7554/elife.68312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
Correct 3’end processing of mRNAs is one of the regulatory cornerstones of gene expression. In a parasite that must adapt to the regulatory requirements of its multi-host life style, there is a need to adopt additional means to partition the distinct transcriptional signatures of the closely and tandemly arranged stage-specific genes. In this study, we report our findings in T. gondii of an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at these loci. We identify the core polyadenylation complex within T. gondii and establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of the T. gondii CPSF4-YTH in complex with an m6A-modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition is associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant model Arabidopsis thaliana. Nanopore direct RNA sequencing shows the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in both T. gondii and A. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in both T. gondii and A. thaliana, as a guardian against aberrant transcriptional read-throughs.
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Affiliation(s)
- Dayana C Farhat
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | | | | | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), Perpignan, France
| | - Lucid Belmudes
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, Grenoble, France
| | - Charlotte Corrao
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Alexandre Bougdour
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), Perpignan, France
| | - Mohamed-Ali Hakimi
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | - Christopher Swale
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
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11
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Courtney DG. Post-Transcriptional Regulation of Viral RNA through Epitranscriptional Modification. Cells 2021; 10:1129. [PMID: 34066974 DOI: 10.3390/cells10051129] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022] Open
Abstract
The field of mRNA modifications has been steadily growing in recent years as technologies have improved and the importance of these residues became clear. However, a subfield has also arisen, specifically focused on how these modifications affect viral RNA, with the possibility that viruses can also be used as a model to best determine the role that these modifications play on cellular mRNAs. First, virologists focused on the most abundant internal mRNA modification, m6A, mapping this modification and elucidating its effects on the RNA of a wide range of RNA and DNA viruses. Next, less common RNA modifications including m5C, Nm and ac4C were investigated and also found to be present on viral RNA. It now appears that viral RNA is littered with a multitude of RNA modifications. In biological systems that are under constant evolutionary pressure to out compete both the host as well as newly arising viral mutants, it poses an interesting question about what evolutionary benefit these modifications provide as it seems evident, at least to this author, that these modifications have been selected for. In this review, I discuss how RNA modifications are identified on viral RNA and the roles that have now been uncovered for these modifications in regard to viral replication. Finally, I propose some interesting avenues of research that may shed further light on the exact role that these modifications play in viral replication.
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12
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Garcia-Outeiral V, de la Parte C, Fidalgo M, Guallar D. The Complexity of TET2 Functions in Pluripotency and Development. Front Cell Dev Biol 2021; 8:630754. [PMID: 33537318 PMCID: PMC7848104 DOI: 10.3389/fcell.2020.630754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Ten-eleven translocation-2 (TET2) is a crucial driver of cell fate outcomes in a myriad of biological processes, including embryonic development and tissue homeostasis. TET2 catalyzes the demethylation of 5-methylcytosine on DNA, affecting transcriptional regulation. New exciting research has provided evidence for TET2 catalytic activity in post-transcriptional regulation through RNA hydroxymethylation. Here we review the current understanding of TET2 functions on both DNA and RNA, and the influence of these chemical modifications in normal development and pluripotency contexts, highlighting TET2 versatility in influencing genome regulation and cellular phenotypes.
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Affiliation(s)
- Vera Garcia-Outeiral
- Stem Cells and Human Diseases Group, Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristina de la Parte
- Epitranscriptomics and Ageing Group, Department of Biochemistry and Molecular Biology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Fidalgo
- Stem Cells and Human Diseases Group, Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Diana Guallar
- Epitranscriptomics and Ageing Group, Department of Biochemistry and Molecular Biology, Center for Research in Molecular Medicine and Chronic Diseases, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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13
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Leonetti AM, Chu MY, Ramnaraign FO, Holm S, Walters BJ. An Emerging Role of m6A in Memory: A Case for Translational Priming. Int J Mol Sci 2020; 21:E7447. [PMID: 33050279 DOI: 10.3390/ijms21207447] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022] Open
Abstract
Investigation into the role of methylation of the adenosine base (m6A) of RNA has only recently begun, but it quickly became apparent that m6A is able to control and fine-tune many aspects of mRNA, from splicing to translation. The ability of m6A to regulate translation distally, away from traditional sites near the nucleus, quickly caught the eye of neuroscientists because of implications for selective protein translation at synapses. Work in the brain has demonstrated how m6A is functionally required for many neuronal functions, but two in particular are covered at length here: The role of m6A in 1) neuron development; and 2) memory formation. The purpose of this review is not to cover all data about m6A in the brain. Instead, this review will focus on connecting mechanisms of m6A function in neuron development, with m6A’s known function in memory formation. We will introduce the concept of “translational priming” and discuss how current data fit into this model, then speculate how m6A-mediated translational priming during memory consolidation can regulate learning and memory locally at the synapse.
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14
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Huang H, Camats-Perna J, Medeiros R, Anggono V, Widagdo J. Altered Expression of the m6A Methyltransferase METTL3 in Alzheimer's Disease. eNeuro 2020; 7:ENEURO. [PMID: 32847866 DOI: 10.1523/ENEURO.0125-20.2020] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/27/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Cognitive impairment in Alzheimer’s disease (AD) is associated with dysregulation of the RNA and protein expression profiles in the brain. Recent studies have highlighted the importance of RNA post-transcriptional regulation (epitranscriptomics) in higher order brain functions. Specifically, N6-methyladenosine (m6A), which controls RNA stability, splicing, translation and trafficking, plays an important role in learning and memory. This raises the question of whether m6A signaling is perturbed in AD. To address this, we investigated the expression profile of known m6A-regulatory genes using a public RNA-seq dataset and identified a subset of genes which were significantly dysregulated in the human AD brain. Among these, genes encoding the m6A methyltransferase, METTL3, and a member of the m6A methyltransferase complex (MACOM), RBM15B, were downregulated and upregulated in the hippocampus, respectively. These findings were validated at the protein level using an independent cohort of postmortem human brain samples. Unexpectedly, we observed an accumulation of methyltransferase-like 3 (METTL3), but not RBM15B, in the insoluble fractions, which positively correlated with the levels of insoluble Tau protein in the postmortem human AD samples. Aberrant expression and distribution of METTL3 in the hippocampus of the AD brain may therefore represent an epitranscriptomic mechanism underlying the altered gene expression patterns associated with disease pathogenesis.
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15
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Tsai K, Jaguva Vasudevan AA, Martinez Campos C, Emery A, Swanstrom R, Cullen BR. Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability. Cell Host Microbe 2020; 28:306-312.e6. [PMID: 32533923 DOI: 10.1016/j.chom.2020.05.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/21/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
Epitranscriptomic RNA modifications, including methylation of adenine and cytidine residues, are now recognized as key regulators of both cellular and viral mRNA function. Moreover, acetylation of the N4 position of cytidine (ac4C) was recently reported to increase the translation and stability of cellular mRNAs. Here, we show that ac4C and N-acetyltransferase 10 (NAT10), the enzyme that adds ac4C to RNAs, have been subverted by human immunodeficiency virus 1 (HIV-1) to increase viral gene expression. HIV-1 transcripts are modified with ac4C at multiple discrete sites, and silent mutagenesis of these ac4C sites led to decreased HIV-1 gene expression. Similarly, loss of ac4C from viral transcripts due to depletion of NAT10 inhibited HIV-1 replication by reducing viral RNA stability. Interestingly, the NAT10 inhibitor remodelin could inhibit HIV-1 replication at concentrations that have no effect on cell viability, thus identifying ac4C addition as a potential target for antiviral drug development.
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16
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Valle C, Martin B, Debart F, Vasseur JJ, Imbert I, Canard B, Coutard B, Decroly E. The C-Terminal Domain of the Sudan Ebolavirus L Protein Is Essential for RNA Binding and Methylation. J Virol 2020; 94:e00520-20. [PMID: 32269120 DOI: 10.1128/JVI.00520-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 03/29/2020] [Indexed: 12/20/2022] Open
Abstract
The large (L) protein of Ebola virus is a key protein for virus replication. Its N-terminal region harbors the RNA-dependent RNA polymerase activity, and its C terminus contains a cap assembling line composed of a capping domain and a methyltransferase domain (MTase) followed by a C-terminal domain (CTD) of unknown function. The L protein MTase catalyzes methylation at the 2'-O and N-7 positions of the cap structures. In addition, the MTase of Ebola virus can induce cap-independent internal adenosine 2'-O-methylation. In this work, we investigated the CTD role in the regulation of the cap-dependent and cap-independent MTase activities of the L protein. We found that the CTD, which is enriched in basic amino acids, plays a key role in RNA binding and in turn regulates the different MTase activities. We demonstrated that the mutation of CTD residues modulates specifically the different MTase activities. Altogether, our results highlight the pivotal role of the L protein CTD in the control of viral RNA methylation, which is critical for Ebola virus replication and escape from the innate response in infected cells.IMPORTANCE Ebola virus infects human and nonhuman primates, causing severe infections that are often fatal. The epidemics, in West and Central Africa, emphasize the urgent need to develop antiviral therapies. The Ebola virus large protein (L), which is the central protein for viral RNA replication/transcription, harbors a methyltransferase domain followed by a C-terminal domain of unknown function. We show that the C-terminal domain regulates the L protein methyltransferase activities and consequently participates in viral replication and escape of the host innate immunity.
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17
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Shen S, Sun X. Emerging role of mRNA epitranscriptomic regulation in chemoresistant cancer cells. Mol Cell Oncol 2020; 7:1728467. [PMID: 32391421 PMCID: PMC7199735 DOI: 10.1080/23723556.2020.1728467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 06/11/2023]
Abstract
Cancer persister cells remain a significant barrier to effective anti-cancer therapy. We found that melanoma persister cells undergo a reversible reprogramming of mRNA translation. A subset of mRNAs, harboring N6-methyladenosine in their 5'-untranslated regions, is translationally up-regulated in an eIF4A-dependent manner. Targeting eIF4A prevents the emergence of resistant clones.
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Affiliation(s)
- Shensi Shen
- Inserm U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - Xiaoxiao Sun
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
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18
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Wu J, Frazier K, Zhang J, Gan Z, Wang T, Zhong X. Emerging role of m 6 A RNA methylation in nutritional physiology and metabolism. Obes Rev 2020; 21:e12942. [PMID: 31475777 PMCID: PMC7427634 DOI: 10.1111/obr.12942] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022]
Abstract
N6 -methyladenine (m6 A) is the most prevalent type of internal RNA methylation in eukaryotic mRNA and plays critical roles in regulating gene expression for fundamental cellular processes and diverse physiological functions. Recent evidence indicates that m6 A methylation regulates physiology and metabolism, and m6 A has been increasingly implicated in a variety of human diseases, including obesity, diabetes, metabolic syndrome and cancer. Conversely, nutrition and diet can modulate or reverse m6 A methylation patterns on gene expression. In this review, we summarize the recent progress in the study of the m6 A methylation mechanisms and highlight the crosstalk between m6 A modification, nutritional physiology and metabolism.
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Affiliation(s)
- Jiamin Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Katya Frazier
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Jingfei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhending Gan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tian Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiang Zhong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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19
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Courtney DG, Tsai K, Bogerd HP, Kennedy EM, Law BA, Emery A, Swanstrom R, Holley CL, Cullen BR. Epitranscriptomic Addition of m(5)C to HIV-1 Transcripts Regulates Viral Gene Expression. Cell Host Microbe 2019; 26:217-227.e6. [PMID: 31415754 DOI: 10.1016/j.chom.2019.07.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/30/2019] [Accepted: 07/16/2019] [Indexed: 01/12/2023]
Abstract
How the covalent modification of mRNA ribonucleotides, termed epitranscriptomic modifications, alters mRNA function remains unclear. One issue has been the difficulty of quantifying these modifications. Using purified HIV-1 genomic RNA, we show that this RNA bears more epitranscriptomic modifications than the average cellular mRNA, with 5-methylcytosine (m5C) and 2'O-methyl modifications being particularly prevalent. The methyltransferase NSUN2 serves as the primary writer for m5C on HIV-1 RNAs. NSUN2 inactivation inhibits not only m5C addition to HIV-1 transcripts but also viral replication. This inhibition results from reduced HIV-1 protein, but not mRNA, expression, which in turn correlates with reduced ribosome binding to viral mRNAs. In addition, loss of m5C dysregulates the alternative splicing of viral RNAs. These data identify m5C as a post-transcriptional regulator of both splicing and function of HIV-1 mRNA, thereby affecting directly viral gene expression.
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20
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Courtney DG, Chalem A, Bogerd HP, Law BA, Kennedy EM, Holley CL, Cullen BR. Extensive Epitranscriptomic Methylation of A and C Residues on Murine Leukemia Virus Transcripts Enhances Viral Gene Expression. mBio 2019; 10:e01209-19. [PMID: 31186331 PMCID: PMC6561033 DOI: 10.1128/mbio.01209-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 01/01/2023] Open
Abstract
While it has been known for several years that viral RNAs are subject to the addition of several distinct covalent modifications to individual nucleotides, collectively referred to as epitranscriptomic modifications, the effect of these editing events on viral gene expression has been controversial. Here, we report the purification of murine leukemia virus (MLV) genomic RNA to homogeneity and show that this viral RNA contains levels of N6-methyladenosine (m6A), 5-methylcytosine (m5C), and 2'O-methylated (Nm) ribonucleotides that are an order of magnitude higher than detected on bulk cellular mRNAs. Mapping of m6A and m5C residues on MLV transcripts identified multiple discrete editing sites and allowed the construction of MLV variants bearing silent mutations that removed a subset of these sites. Analysis of the replication potential of these mutants revealed a modest but significant attenuation in viral replication in 3T3 cells in culture. Consistent with a positive role for m6A and m5C in viral replication, we also demonstrate that overexpression of the key m6A reader protein YTHDF2 enhances MLV replication, while downregulation of the m5C writer NSUN2 inhibits MLV replication.IMPORTANCE The data presented in the present study demonstrate that MLV RNAs bear an exceptionally high level of the epitranscriptomic modifications m6A, m5C, and Nm, suggesting that these each facilitate some aspect of the viral replication cycle. Consistent with this hypothesis, we demonstrate that mutational removal of a subset of these m6A or m5C modifications from MLV transcripts inhibits MLV replication in cis, and a similar result was also observed upon manipulation of the level of expression of key cellular epitranscriptomic cofactors in trans Together, these results argue that the addition of several different epitranscriptomic modifications to viral transcripts stimulates viral gene expression and suggest that MLV has therefore evolved to maximize the level of these modifications that are added to viral RNAs.
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Affiliation(s)
- David G Courtney
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Andrea Chalem
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Brittany A Law
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Edward M Kennedy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher L Holley
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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21
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Widagdo J, Anggono V. The m6A- epitranscriptomic signature in neurobiology: from neurodevelopment to brain plasticity. J Neurochem 2018; 147:137-152. [PMID: 29873074 DOI: 10.1111/jnc.14481] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022]
Abstract
Research over the past decade has provided strong support for the importance of various epigenetic mechanisms, including DNA and histone modifications in regulating activity-dependent gene expression in the mammalian central nervous system. More recently, the emerging field of epitranscriptomics revealed an equally important role of post-transcriptional RNA modifications in shaping the transcriptomic landscape of the brain. This review will focus on the methylation of the adenosine base at the N6 position, termed N6 methyladenosine (m6A), which is the most abundant internal modification that decorates eukaryotic messenger RNAs. Given its prevalence and dynamic regulation in the adult brain, the m6A-epitranscriptome provides an additional layer of regulation on RNA that can be controlled in a context- and stimulus-dependent manner. Conceptually, m6A serves as a molecular switch that regulates various aspects of RNA function, including splicing, stability, localization, or translational control. The versatility of m6A function is typically determined through interaction or disengagement with specific classes of m6A-interacting proteins. Here we review recent advances in the field and provide insights into the roles of m6A in regulating brain function, from development to synaptic plasticity, learning, and memory. We also discuss how aberrant m6A signaling may contribute to neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
- Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
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22
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Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Howcroft TK, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E. RNA editing, epitranscriptomics, and processing in cancer progression. Cancer Biol Ther 2015; 16:21-7. [PMID: 25455629 DOI: 10.4161/15384047.2014.987555] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The transcriptome is extensively and dynamically regulated by a network of RNA modifying factors. RNA editing enzymes APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) and ADAR (adenosine deaminase, RNA-specific) irreversibly recode primary RNA sequences, whereas newly described methylases (writers) and de-methylases (erasers) dynamically alter RNA molecules in response to environmental conditions. RNA modifications can affect RNA splicing, nuclear-cytoplasmic transport, translation, and regulation of gene expression by RNA interference. In addition, tRNA base modifications, processing, and regulated cleavage have been shown to alter global patterns of mRNA translation in response to cellular stress pathways. Recent studies, some of which were discussed at this workshop, have rekindled interest in the emerging roles of RNA modifications in health and disease. On September 10th, 2014, the Division of Cancer Biology, NCI sponsored a workshop to explore the role of epitranscriptomic RNA modifications and tRNA processing in cancer progression. The workshop attendees spanned a scientific range including chemists, virologists, and RNA and cancer biologists. The goal of the workshop was to explore the interrelationships between RNA editing, epitranscriptomics, and RNA processing and the enzymatic pathways that regulate these activities in cancer initiation and progression. At the conclusion of the workshop, a general discussion focused on defining the major challenges and opportunities in this field, as well as identifying the tools, technologies, resources and community efforts required to accelerate research in this emerging area.
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Affiliation(s)
- Keren L Witkin
- a Division of Cancer Biology; National Cancer Institute ; Bethesda , MD USA
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