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Park ZM, Belnap E, Remillard M, Rose MD. Vir1p, the Yeast Homolog of Virilizer, is Required for mRNA m 6 A Methylation and Meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527493. [PMID: 36798303 PMCID: PMC9934557 DOI: 10.1101/2023.02.07.527493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
N 6 -Methyladenosine (m 6 A) is one of the most abundant modifications found on eukaryotic mRNAs. mRNA methylation regulates a host of biological processes including meiosis, a specialized diploid cell division program that results in the formation of haploid cells (gametes). During budding yeast meiosis, m 6 A levels peak early, before the initiation of the meiotic divisions. High-throughput studies and work from our lab showed that Ygl036wp, a previously uncharacterized protein interacts with Kar4p, a meiotic protein required for mRNA m 6 A-methylation. Ygl036wp has no discernable domains except for several intrinsically disordered regions. However, protein folding prediction tools showed that Ygl036wp folds like VIRMA/Virilizer/VIR, which is involved in mRNA m 6 A-methylation in higher eukaryotes. In addition, Ygl036wp has several conserved motifs shared with VIRMA/Virilizer/VIR proteins. Accordingly, we propose to call the gene VIR1 for budding yeast ortholog of VIR MA/Virilizer/VIR 1 . In support, Vir1p interacts with all other members of the yeast methyltransferase complex and is required for mRNA m 6 A methylation and meiosis. Vir1p is required for the stability of proteins comprising the methyltransferase complex, suggesting that Vir1p acts as a scaffold to stabilize the complex. The vir1 Δ/Δ mutant is defective for premeiotic S-phase, which is suppressed by overexpression of the early meiotic transcription factor IME1; additional overexpression of the translational regulator RIM4 is required for sporulation. Consistent with IME1 suppression, vir1 Δ/Δ exhibits a defect in the abundance of IME1 mRNA, as well as transcripts within Ime1p's regulon. Suppression by IME1 revealed a defect in the expression of the middle meiotic transcription factor, Ndt80p (and genes in its regulon), which is rescued by additional overexpression of RIM4 . Together, these data suggest that Vir1p is required for cells to initiate the meiotic program and for progression through the meiotic divisions and spore formation. Author Summary Ygl036wp is a previously uncharacterized protein that we propose to name Vir1p (budding yeast ortholog of VIR MA/Virilizer/VIR 1 ). Work from our lab and others initially found an interaction between Vir1p and members of the yeast mRNA methyltransferase complex (Kar4p and Mum2p). We found that Vir1p interacts with all known members of the methyltransferase complex and is required for mRNA methylation. Vir1p is required early in meiosis; vir1 Δ/Δ mutants arrest due to the reduced expression of Ime1p. Lower levels of Ime1p cause severe disruption to the meiotic transcriptome in vir1 Δ/Δ. The vir1 Δ/Δ meiotic defect can be partially suppressed by the overexpression of IME1 ; full suppression requires overexpression of both IME1 and RIM4 . Using recent advances in protein folding predictions, we found that Vir1p is a remote homolog of VIRMA/Virilizer/VIR and shares conserved motifs with the protein from other organisms. Vir1p, like VIRMA/Virilizer/VIR, stabilizes the methyltransferase complex.
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Affiliation(s)
- Zachory M. Park
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington DC, 20057, USA
| | - Matthew Remillard
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Mark D. Rose
- Department of Biology, Georgetown University, Washington DC, 20057, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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Li H, Zhang Q, Feng Q, You Q, Guo X. The development of small molecules targeting methyltransferase-like 3. Drug Discov Today 2023; 28:103513. [PMID: 36736582 DOI: 10.1016/j.drudis.2023.103513] [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: 10/11/2022] [Revised: 12/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
In mammals, N6-methyladenosine (m6A) is thought to be the most common and conserved mRNA modification. Methyltransferase-like 3 (METTL3) is the primary regulator of m6A methyl-transformed modification. Small molecules targeting METTL3 could be effective therapeutics for many disorders, given that a large body of research has linked METTL3 dysregulation with a variety of diseases and altered physiological states, especially with the growth and initiation of cancer. Here, we systematically reviewed the discovery of small molecules targeting METTL3, as well as their future development, for researchers studying in the field.
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Affiliation(s)
- Hongyu Li
- Jiang Su Key Laboratory of Drug Design and Optimization and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Qinglan Feng
- Jiang Su Key Laboratory of Drug Design and Optimization and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiaoke Guo
- Jiang Su Key Laboratory of Drug Design and Optimization and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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The Repertoire of RNA Modifications Orchestrates a Plethora of Cellular Responses. Int J Mol Sci 2023; 24:ijms24032387. [PMID: 36768716 PMCID: PMC9916637 DOI: 10.3390/ijms24032387] [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: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Although a plethora of DNA modifications have been extensively investigated in the last decade, recent breakthroughs in molecular biology, including high throughput sequencing techniques, have enabled the identification of post-transcriptional marks that decorate RNAs; hence, epitranscriptomics has arisen. This recent scientific field aims to decode the regulatory layer of the transcriptome and set the ground for the detection of modifications in ribose nucleotides. Until now, more than 170 RNA modifications have been reported in diverse types of RNA that contribute to various biological processes, such as RNA biogenesis, stability, and transcriptional and translational accuracy. However, dysfunctions in the RNA-modifying enzymes that regulate their dynamic level can lead to human diseases and cancer. The present review aims to highlight the epitranscriptomic landscape in human RNAs and match the catalytic proteins with the deposition or deletion of a specific mark. In the current review, the most abundant RNA modifications, such as N6-methyladenosine (m6A), N5-methylcytosine (m5C), pseudouridine (Ψ) and inosine (I), are thoroughly described, their functional and regulatory roles are discussed and their contributions to cellular homeostasis are stated. Ultimately, the involvement of the RNA modifications and their writers, erasers, and readers in human diseases and cancer is also discussed.
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Lothion-Roy J, Haigh DB, Harris AE, Metzler VM, Alsaleem M, Toss MS, Kariri Y, Ntekim A, Robinson BD, Khani F, Gudas LJ, Allegrucci C, James VH, Madhusudan S, Mather M, Emes RD, Archer N, Fray RG, Rakha E, Jeyapalan JN, Rutland CS, Mongan NP, Woodcock CL. Clinical and molecular significance of the RNA m 6A methyltransferase complex in prostate cancer. Front Genet 2023; 13:1096071. [PMID: 36733939 PMCID: PMC9887525 DOI: 10.3389/fgene.2022.1096071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal mRNA modification and is dynamically regulated through distinct protein complexes that methylate, demethylate, and/or interpret the m6A modification. These proteins, and the m6A modification, are involved in the regulation of gene expression, RNA stability, splicing and translation. Given its role in these crucial processes, m6A has been implicated in many diseases, including in cancer development and progression. Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous cancer in men and recent studies support a role for m6A in PCa. Despite this, the literature currently lacks an integrated analysis of the expression of key components of the m6A RNA methyltransferase complex, both in PCa patients and in well-established cell line models. For this reason, this study used immunohistochemistry and functional studies to investigate the mechanistic and clinical significance of the METTL3, METTL14, WTAP and CBLL1 components of the m6A methyltransferase complex in PCa specimens and cell lines. Expression of METTL3 and CBLL1, but not METTL14 and WTAP, was associated with poorer PCa patient outcomes. Expression of METTL3, METTL14, WTAP and CBLL1 was higher in PCa cells compared with non-malignant prostate cells, with the highest expression seen in castrate-sensitive, androgen-responsive PCa cells. Moreover, in PCa cell lines, expression of METTL3 and WTAP was found to be androgen-regulated. To investigate the mechanistic role(s) of the m6A methyltransferase complex in PCa cells, short hairpin RNA (shRNA)-mediated knockdown coupled with next generation sequencing was used to determine the transcriptome-wide roles of METTL3, the catalytic subunit of the m6A methyltransferase complex. Functional depletion of METTL3 resulted in upregulation of the androgen receptor (AR), together with 134 AR-regulated genes. METTL3 knockdown also resulted in altered splicing, and enrichment of cell cycle, DNA repair and metabolic pathways. Collectively, this study identified the functional and clinical significance of four essential m6A complex components in PCa patient specimens and cell lines for the first time. Further studies are now warranted to determine the potential therapeutic relevance of METTL3 inhibitors in development to treat leukaemia to benefit patients with PCa.
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Affiliation(s)
- Jennifer Lothion-Roy
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Daisy B. Haigh
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Anna E. Harris
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Veronika M. Metzler
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Mansour Alsaleem
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom,Department of Applied Medical Science, Applied College, Qassim University, Qassim, Saudi Arabia
| | - Michael S. Toss
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Yousif Kariri
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom,Department of Clinical Laboratory Science, Faculty of Applied Medical Science, Shaqra University, Shaqra, Saudi Arabia
| | - Atara Ntekim
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom,Department of Radiation Oncology, University Hospital Ibadan, University of Ibadan, Ibadan, Nigeria
| | - Brian D. Robinson
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Francesca Khani
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
| | - Cinzia Allegrucci
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Victoria H. James
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Srinivasan Madhusudan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Melissa Mather
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Richard D. Emes
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nathan Archer
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Rupert G. Fray
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Emad Rakha
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Jennie N. Jeyapalan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Catrin S. Rutland
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nigel P. Mongan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom,Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States,*Correspondence: Nigel P. Mongan, , ; Corinne L. Woodcock,
| | - Corinne L. Woodcock
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom,*Correspondence: Nigel P. Mongan, , ; Corinne L. Woodcock,
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Shu Y, Guo Y, Zheng Y, He S, Shi Z. RNA methylation in vascular disease: a systematic review. J Cardiothorac Surg 2022; 17:323. [PMID: 36536469 PMCID: PMC9762007 DOI: 10.1186/s13019-022-02077-1] [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: 07/12/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Despite the rise in morbidity and mortality associated with vascular diseases, the underlying pathophysiological molecular mechanisms are still unclear. RNA N6-methyladenosine modification, as the most common cellular mechanism of RNA regulation, participates in a variety of biological functions and plays an important role in epigenetics. A large amount of evidence shows that RNA N6-methyladenosine modifications play a key role in the morbidity caused by vascular diseases. Further research on the relationship between RNA N6-methyladenosine modifications and vascular diseases is necessary to understand disease mechanisms at the gene level and to provide new tools for diagnosis and treatment. In this study, we summarize the currently available data on RNA N6-methyladenosine modifications in vascular diseases, addressing four aspects: the cellular regulatory system of N6-methyladenosine methylation, N6-methyladenosine modifications in risk factors for vascular disease, N6-methyladenosine modifications in vascular diseases, and techniques for the detection of N6-methyladenosine-methylated RNA.
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Affiliation(s)
- Yue Shu
- Geriatric Multi-Clinic Center, Hainan ChengMei Hospital, Haikou, Hainan People’s Republic of China ,Department of Special Medical Services, Hainan Cancer Hospital, Haikou, Hainan People’s Republic of China
| | - Yilong Guo
- grid.488137.10000 0001 2267 2324Medical School of Chinese PLA, Beijing, People’s Republic of China ,grid.414252.40000 0004 1761 8894Department of Vascular and Endovascular Surgery, The First Medical Centre of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yin Zheng
- Geriatric Multi-Clinic Center, Hainan ChengMei Hospital, Haikou, Hainan People’s Republic of China ,Department of Special Medical Services, Hainan Cancer Hospital, Haikou, Hainan People’s Republic of China
| | - Shuwu He
- grid.443397.e0000 0004 0368 7493Department of Cardiovascular Surgery, The Second Affiliated Hospital of Hainan Medical University, 48th of Bai Shui Tang Road, Haikou, 570311 Hainan People’s Republic of China
| | - Zhensu Shi
- grid.443397.e0000 0004 0368 7493Department of Cardiovascular Surgery, The Second Affiliated Hospital of Hainan Medical University, 48th of Bai Shui Tang Road, Haikou, 570311 Hainan People’s Republic of China
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WTAP Targets the METTL3 m 6A-Methyltransferase Complex to Cytoplasmic Hepatitis C Virus RNA to Regulate Infection. J Virol 2022; 96:e0099722. [PMID: 36314819 PMCID: PMC9683008 DOI: 10.1128/jvi.00997-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Modification of the hepatitis C virus (HCV) positive-strand RNA genome by N6-methyladenosine (m6A) regulates the viral life cycle. This life cycle takes place solely in the cytoplasm, while m6A addition on cellular mRNA takes place in the nucleus. Thus, the mechanisms by which m6A is deposited on the viral RNA have been unclear. In this work, we find that m6A modification of HCV RNA by the m6A-methyltransferase proteins methyltransferase-like 3 and 14 (METTL3 and METTL14) is regulated by Wilms' tumor 1-associating protein (WTAP). WTAP, a predominantly nuclear protein, is an essential member of the cellular mRNA m6A-methyltransferase complex and known to target METTL3 to mRNA. We found that HCV infection induces localization of WTAP to the cytoplasm. Importantly, we found that WTAP is required for both METTL3 interaction with HCV RNA and m6A modification across the viral RNA genome. Further, we found that WTAP, like METTL3 and METTL14, negatively regulates the production of infectious HCV virions, a process that we have previously shown is regulated by m6A. Excitingly, WTAP regulation of both HCV RNA m6A modification and virion production was independent of its ability to localize to the nucleus. Together, these results reveal that WTAP is critical for HCV RNA m6A modification by METTL3 and METTL14 in the cytoplasm. IMPORTANCE Positive-strand RNA viruses such as HCV represent a significant global health burden. Previous work has described that HCV RNA contains the RNA modification m6A and how this modification regulates viral infection. Yet, how this modification is targeted to HCV RNA has remained unclear due to the incompatibility of the nuclear cellular processes that drive m6A modification with the cytoplasmic HCV life cycle. In this study, we present evidence for how m6A modification is targeted to HCV RNA in the cytoplasm by a mechanism in which WTAP recruits the m6A-methyltransferase METTL3 to HCV RNA. This targeting strategy for m6A modification of cytoplasmic RNA viruses is likely relevant for other m6A-modified positive-strand RNA viruses with cytoplasmic life cycles such as enterovirus 71 and SARS-CoV-2 and provides an exciting new target for potential antiviral therapies.
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Comprehensive Analysis Revealed the Potential Roles of N6-Methyladenosine (m6A) Mediating E. coli F18 Susceptibility in IPEC-J2 Cells. Int J Mol Sci 2022; 23:ijms232113602. [DOI: 10.3390/ijms232113602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Post-weaning diarrhea caused by enterotoxigenic Escherichia coli F18 (E. coli F18) causes significant economic losses for pig producers. N6-methyladenosine (m6A) is a highly abundant epitranscriptomic marker that has been found to be involved in regulating the resistance of host cells to pathogenic infection, but its potential role in E. coli F18-exposed intestinal porcine epithelial cells (IPEC-J2) remains undetermined. Here, we demonstrated that m6A and its regulators modulate E. coli F18 susceptibility. Briefly, we revealed that the Wilms’ tumor 1-associating protein (WTAP) expressions were markedly elevated in IPEC-J2 cells upon E. coli F18 exposure. WTAP are required for the regulation of E. coli F18 adhesion in IPEC-J2 cells. Additionally, WTAP knockdown significantly suppressed m6A level at N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (GCNT2) 3′UTR, resulting in the enhancement of TH N6-methyladenosine RNA binding protein 2 (YTHDF2)-mediated GCNT2 mRNA stability. Subsequently, the altered GCNT2 expressions could inhibit the glycosphingolipid biosynthesis, thus improving resistance to E. coli F18 infection in IPEC-J2. Collectively, our analyses highlighted the mechanism behind the m6A-mediated management of E. coli F18 susceptibility, which will aid in the development of novel approaches that protect against bacterial diarrhea in piglets.
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Wang Z, Zhou J, Zhang H, Ge L, Li J, Wang H. RNA m 6 A methylation in cancer. Mol Oncol 2022; 17:195-229. [PMID: 36260366 PMCID: PMC9892831 DOI: 10.1002/1878-0261.13326] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 02/04/2023] Open
Abstract
N6 -methyladenosine (m6 A) is one of the most abundant internal modifications in eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). It is a reversible and dynamic RNA modification that has been observed in both internal coding segments and untranslated regions. Studies indicate that m6 A modifications play important roles in translation, RNA splicing, export, degradation and ncRNA processing control. In this review, we focus on the profiles and biological functions of RNA m6 A methylation on both mRNAs and ncRNAs. The dynamic modification of m6 A and its potential roles in cancer development are discussed. Moreover, we discuss the possibility of m6 A modifications serving as potential biomarkers for cancer diagnosis and targets for therapy.
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Affiliation(s)
- Zhaotong Wang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Jiawang Zhou
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Haisheng Zhang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Lichen Ge
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Jiexin Li
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Hongsheng Wang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
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Su S, Li S, Deng T, Gao M, Yin Y, Wu B, Peng C, Liu J, Ma J, Zhang K. Cryo-EM structures of human m 6A writer complexes. Cell Res 2022; 32:982-994. [PMID: 36167981 PMCID: PMC9652331 DOI: 10.1038/s41422-022-00725-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The m6A "writer" consists of the catalytic subunit m6A-METTL complex (MAC) and the regulatory subunit m6A-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the m6A writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and m6A methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active m6A writer complex.
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Affiliation(s)
- Shichen Su
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shanshan Li
- grid.59053.3a0000000121679639MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Ting Deng
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Minsong Gao
- grid.13402.340000 0004 1759 700XMOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang China
| | - Yue Yin
- grid.458506.a0000 0004 0497 0637National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Baixing Wu
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Chao Peng
- grid.458506.a0000 0004 0497 0637National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Jianzhao Liu
- grid.13402.340000 0004 1759 700XMOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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The RNA m 6A writer WTAP in diseases: structure, roles, and mechanisms. Cell Death Dis 2022; 13:852. [PMID: 36207306 PMCID: PMC9546849 DOI: 10.1038/s41419-022-05268-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/05/2022]
Abstract
N6-methyladenosine (m6A) is a widely investigated RNA modification in studies on the "epigenetic regulation" of mRNAs that is ubiquitously present in eukaryotes. Abnormal changes in m6A levels are closely related to the regulation of RNA metabolism, heat shock stress, tumor occurrence, and development. m6A modifications are catalyzed by the m6A writer complex, which contains RNA methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14), Wilms tumor 1-associated protein (WTAP), and other proteins with methyltransferase (MTase) capability, such as RNA-binding motif protein 15 (RBM15), KIAA1429 and zinc finger CCCH-type containing 13 (ZC3H13). Although METTL3 is the main catalytic subunit, WTAP is a regulatory subunit whose function is to recruit the m6A methyltransferase complex to the target mRNA. Specifically, WTAP is required for the accumulation of METTL3 and METTL14 in nuclear speckles. In this paper, we briefly introduce the molecular mechanism of m6A modification. Then, we focus on WTAP, a component of the m6A methyltransferase complex, and introduce its structure, localization, and physiological functions. Finally, we describe its roles and mechanisms in cancer.
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The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer. Cell Mol Neurobiol 2022:10.1007/s10571-022-01283-8. [DOI: 10.1007/s10571-022-01283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/04/2022] [Indexed: 11/03/2022]
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RNA methylation in immune cells. Adv Immunol 2022; 155:39-94. [PMID: 36357012 DOI: 10.1016/bs.ai.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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63
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Fan Y, Li X, Sun H, Gao Z, Zhu Z, Yuan K. Role of WTAP in Cancer: From Mechanisms to the Therapeutic Potential. Biomolecules 2022; 12:biom12091224. [PMID: 36139062 PMCID: PMC9496264 DOI: 10.3390/biom12091224] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/16/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Wilms' tumor 1-associating protein (WTAP) is required for N6-methyladenosine (m6A) RNA methylation modifications, which regulate biological processes such as RNA splicing, cell proliferation, cell cycle, and embryonic development. m6A is the predominant form of mRNA modification in eukaryotes. WTAP exerts m6A modification by binding to methyltransferase-like 3 (METTL3) in the nucleus to form the METTL3-methyltransferase-like 14 (METTL14)-WTAP (MMW) complex, a core component of the methyltransferase complex (MTC), and localizing to the nuclear patches. Studies have demonstrated that WTAP plays a critical role in various cancers, both dependent and independent of its role in m6A modification of methyltransferases. Here, we describe the recent findings on the structural features of WTAP, the mechanisms by which WTAP regulates the biological functions, and the molecular mechanisms of its functions in various cancers. By summarizing the latest WTAP research, we expect to provide new directions and insights for oncology research and discover new targets for cancer treatment.
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Affiliation(s)
- Yongfei Fan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Xinwei Li
- Department of Gastroenterology, Affiliated Cancer Hospital of Bengbu Medical College, Bengbu 233000, China
| | - Huihui Sun
- Department of Radiotherapy, The Affiliated Changzhou No. 1 People’s Hospital of Suzhou University, Changzhou 213003, China
| | - Zhaojia Gao
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Zheng Zhu
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Kai Yuan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Correspondence:
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64
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Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry 2022; 27:3633-3646. [PMID: 35474104 PMCID: PMC9596619 DOI: 10.1038/s41380-022-01570-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
Distinct cell types are generated at specific times during brain development and are regulated by epigenetic, transcriptional, and newly emerging epitranscriptomic mechanisms. RNA modifications are known to affect many aspects of RNA metabolism and have been implicated in the regulation of various biological processes and in disease. Recent studies imply that dysregulation of the epitranscriptome may be significantly associated with neuropsychiatric, neurodevelopmental, and neurodegenerative disorders. Here we review the current knowledge surrounding the role of the RNA modifications N6-methyladenosine, 5-methylcytidine, pseudouridine, A-to-I RNA editing, 2'O-methylation, and their associated machinery, in brain development and human diseases. We also highlight the need for the development of new technologies in the pursuit of directly mapping RNA modifications in both genome- and single-molecule-level approach.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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65
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Huang X, Abuduwaili N, Wang X, Tao M, Wang X, Huang G. Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development. Int J Mol Sci 2022; 23:ijms23179887. [PMID: 36077287 PMCID: PMC9456376 DOI: 10.3390/ijms23179887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m6A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m6A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m6A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways.
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Affiliation(s)
- Xiaoyu Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Nigara Abuduwaili
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumuqi 830054, China
| | - Xinting Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Miao Tao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiaoqian Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Gengqing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumuqi 830054, China
- Correspondence:
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66
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Yan Z, Liang P. m6A modification of mRNA in skin diseases. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2022; 47:1154-1162. [PMID: 36097784 PMCID: PMC10950115 DOI: 10.11817/j.issn.1672-7347.2022.210332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A) is the predominant post-transcriptional modification for eukaryotic mRNA. It's regulated by methyltransferases, demethylases, and m6A binding proteins, and plays an important role in regulating splicing, translation, and degradation of mRNA. Skin diseases, especially immune skin diseases and skin tumors, have a complicated pathogenesis and are refractory to treatment, seriously affecting the patient quality of life. Recent studies have revealed that m6A and its regulatory proteins can affect the development of numerous skin diseases. The m6A modification was found to be involved in skin accessory development, including hair follicle and sweat gland formation. The level of m6A modification was significantly altered in a variety of skin diseases including melanoma, cutaneous squamous cell carcinoma, Merkel cell carcinoma, and psoriasis, and affected a variety of biological processes including cell proliferation and differentiation migration. The m6A and its regulatory proteins may become potential molecular markers or therapeutic targets for skin diseases, and have promising clinical applications in early diagnosis, efficacy determination, prognosis prediction, and gene therapy of skin diseases.
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Affiliation(s)
- Zhuoxian Yan
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China.
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67
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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68
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Zhao C, Xu G, Zhang X, Ye Y, Cai W, Shao Q. RNA m6A modification orchestrates the rhythm of immune cell development from hematopoietic stem cells to T and B cells. Front Immunol 2022; 13:839291. [PMID: 35935968 PMCID: PMC9354743 DOI: 10.3389/fimmu.2022.839291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/28/2022] [Indexed: 11/15/2022] Open
Abstract
RNA, one of the major building blocks of the cell, participates in many essential life processes. RNA stability is well-established to be closely related to various RNA modifications. To date, hundreds of different RNA modifications have been identified. N6-methyladenosine (m6A) is one of the most important RNA modifications in mammalian cells. An increasing body of evidence from recently published studies suggests that m6A modification is a novel immune system regulator of the generation and differentiation of hematopoietic stem cells (HSCs) and immune cells. In this review, we introduce the process and relevant regulatory mechanisms of m6A modification; summarize recent findings of m6A in controlling HSC generation and self-renewal, and the development and differentiation of T and B lymphocytes from HSCs; and discuss the potential mechanisms involved.
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Affiliation(s)
- Chuanxiang Zhao
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Guoying Xu
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Xiaoxian Zhang
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Yunfeng Ye
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Qixiang Shao
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
- Reproductive Sciences Institute, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
- *Correspondence: Qixiang Shao,
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69
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Maimaiti A, Tuersunniyazi A, Meng X, Pei Y, Ji W, Feng Z, Jiang L, Wang Z, Kasimu M, Wang Y, Shi X. N6-methyladenosine RNA methylation regulator-related alternative splicing gene signature as prognostic predictor and in immune microenvironment characterization of patients with low-grade glioma. Front Genet 2022; 13:872186. [PMID: 35937991 PMCID: PMC9355308 DOI: 10.3389/fgene.2022.872186] [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: 02/09/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: N6-methyladenosine (m6A) RNA methylation is an important epigenetic modification affecting alternative splicing (AS) patterns of genes to regulate gene expression. AS drives protein diversity and its imbalance may be an important factor in tumorigenesis. However, the clinical significance of m6A RNA methylation regulator-related AS in the tumor microenvironment has not been investigated in low-grade glioma (LGG). Methods: We used 12 m6A methylation modulatory genes (WTAP, FTO, HNRNPC, YTHDF2, YTHDF1, YTHDC2, ALKBH5, YTHDC1, ZC3H13, RBM15, METTL14, and METTL3) from The Cancer Genome Atlas (TCGA) database as well as the TCGA-LGG (n = 502) dataset of AS events and transcriptome data. These data were downloaded and subjected to machine learning, bioinformatics, and statistical analyses, including gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Univariate Cox, the Least Absolute Shrinkage and Selection Operator (LASSO), and multivariable Cox regression were used to develop prognostic characteristics. Prognostic values were validated using Kaplan-Maier survival analysis, proportional risk models, ROC curves, and nomograms. The ESTIMATE package, TIMER database, CIBERSORT method, and ssGSEA algorithm in the R package were utilized to explore the role of the immune microenvironment in LGG. Lastly, an AS-splicing factor (SF) regulatory network was examined in the case of considering the role of SFs in regulating AS events. Results: An aggregate of 3,272 m6A regulator-related AS events in patients with LGG were screened using six machine learning algorithms. We developed eight AS prognostic characteristics based on splice subtypes, which showed an excellent prognostic prediction performance. Furthermore, quantitative prognostic nomograms were developed and showed strong validity in prognostic prediction. In addition, prognostic signatures were substantially associated with tumor immune microenvironment diversity, ICB-related genes, and infiltration status of immune cell subtypes. Specifically, UGP2 has better promise as a prognostic factor for LGG. Finally, splicing regulatory networks revealed the potential functions of SFs. Conclusion: The present research offers a novel perspective on the role of AS in m6A methylation. We reveal that m6A methylation regulator-related AS events can mediate tumor progression through the immune-microenvironment, which could serve as a viable biological marker for clinical stratification of patients with LGG so as to optimize treatment regimens.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | | | - Xianghong Meng
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
| | - Yinan Pei
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Wenyu Ji
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhaohai Feng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Lei Jiang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Maimaitijiang Kasimu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Xin Shi, ; Yongxin Wang,
| | - Xin Shi
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
- *Correspondence: Xin Shi, ; Yongxin Wang,
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70
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TTC22 promotes m6A-mediated WTAP expression and colon cancer metastasis in an RPL4 binding-dependent pattern. Oncogene 2022; 41:3925-3938. [PMID: 35798874 DOI: 10.1038/s41388-022-02402-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 02/08/2023]
Abstract
WTAP, an essential component of the RNA N-6-methyladenosine (m6A) modification complex, guides METLL3-METLL14 heteroduplexes to target RNAs in the nuclear speckles of mammalian cells. Here, we show that TTC22 is widely coexpressed with WTAP and FTO in many human tissues by mining Genotype-Tissue Expression (GTEx) datasets. Our results indicate that the direct interaction of TTC22 with 60S ribosomal protein L4 (RPL4) promotes the binding of WTAP mRNA to RPL4, enhances the stability and translation efficiency of WTAP mRNA, and consequently increases the level of WTAP protein. Also, WTAP mRNA itself is an m6A target and YTHDF1 is characterized as an essential m6A binding protein interacting with m6A-modified WTAP mRNA. TTC22 triggers a positive feedback loop between WTAP expression and WTAP mRNA m6A modification, leading to an increased m6A level in total RNA. The knockdown of RPL4, WTAP, or YTHDF1 expression diminishes the TTC22-induced increase in the m6A level of total RNA. Thus, TTC22 caused dramatic expression changes in genes related to metabolic pathways, ribosomal biogenesis, the RNA spliceosome, and microorganism infections. Importantly, TTC22 upregulates the expression of SNAI1 by increasing m6A level and thus promotes lung metastases of colon cancer cells in mice. In conclusion, our study showed that TTC22 upregulates WTAP and SNAI1 expression, which contributes to TTC22-induced colon cancer metastasis.
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71
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Sacco MT, Bland KM, Horner SM. WTAP targets the METTL3 m 6 A-methyltransferase complex to cytoplasmic hepatitis C virus RNA to regulate infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.27.497872. [PMID: 35794896 PMCID: PMC9258289 DOI: 10.1101/2022.06.27.497872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
UNLABELLED Modification of the hepatitis C virus (HCV) positive-strand RNA genome by N6-methyladenosine (m 6 A) regulates the viral lifecycle. This lifecycle takes place solely in the cytoplasm, while m 6 A addition on cellular mRNA takes place in the nucleus. Thus, the mechanisms by which m 6 A is deposited on the viral RNA have been unclear. In this work, we find that m 6 A modification of HCV RNA by the m 6 A-methyltransferase proteins METTL3 and METTL14 is regulated by WTAP. WTAP, a predominantly nuclear protein, is an essential member of the cellular mRNA m 6 A-methyltransferase complex and known to target METTL3 to mRNA. We found that HCV infection induces localization of WTAP to the cytoplasm. Importantly, we found that WTAP is required for both METTL3 interaction with HCV RNA and for m 6 A modification across the viral RNA genome. Further, we found that WTAP, like METTL3 and METTL14, negatively regulates the production of infectious HCV virions, a process that we have previously shown is regulated by m 6 A. Excitingly, WTAP regulation of both HCV RNA m 6 A modification and virion production were independent of its ability to localize to the nucleus. Together, these results reveal that WTAP is critical for HCV RNA m 6 A modification by METTL3 and METTL14 in the cytoplasm. IMPORTANCE Positive-strand RNA viruses such as HCV represent a significant global health burden. Previous work has described how HCV RNA contains the RNA modification m 6 A and how this modification regulates viral infection. Yet, how this modification is targeted to HCV RNA has remained unclear due to the incompatibility of the nuclear cellular processes that drive m 6 A modification with the cytoplasmic HCV lifecycle. In this study, we present evidence for how m 6 A modification is targeted to HCV RNA in the cytoplasm by a mechanism in which WTAP recruits the m 6 A-methyltransferase METTL3 to HCV RNA. This targeting strategy for m 6 A modification of cytoplasmic RNA viruses is likely relevant for other m 6 A-modified positive-strand RNA viruses with cytoplasmic lifecycles such as enterovirus 71 and SARS-CoV-2 and provides an exciting new target for potential antiviral therapies.
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HIF-1 α Regulated WTAP Overexpression Promoting the Warburg Effect of Ovarian Cancer by m6A-Dependent Manner. J Immunol Res 2022; 2022:6130806. [PMID: 35733918 PMCID: PMC9207020 DOI: 10.1155/2022/6130806] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 12/21/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation has been determined to execute crucial functions in tumorigenesis and cancer development. WT1-associated protein (WTAP) has an important “writer” role in m6A modification, and it is also a nuclear protein that colocalizes with splicing factors and plays a critical role in cell function and cancer progression. However, little is known about the role of WTAP in ovarian cancer (OC) and its mechanisms. In this study, we found for the first time that hypoxia-inducible factor (HIF)-1α could positively regulate increased expression of WTAP under hypoxia. And further results revealed that WTAP expression was closely associated with the clinicopathological features of OC, and high expression of WTAP predicted low survival rate in patients with OC. In addition, cell proliferation and invasive capacity were significantly reduced after knockdown of WTAP expression in OC cells. However, cell proliferation and invasive ability were significantly enhanced after overexpression of WTAP. Additionally, we find that WTAP interacts with DGCR8 (a crucial chip protein) to regulate the expression of microRNA-200 (miR-200) in an m6A-dependent way. Further experiments showed that the key glycolysis enzyme HK2 could be positively regulated by miR-200, which significantly affected the intracellular Warburg effect. In conclusion, this is considered uncovered that upregulation of WTAP expression by HIF-1α intercedes with miRNA processing, accelerates the Warburg impact, and advances the event and advancement of tumor, thus giving a novel viewpoint on m6A adjustment in OC movement.
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73
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Song N, Cui K, Zhang K, Yang J, Liu J, Miao Z, Zhao F, Meng H, Chen L, Chen C, Li Y, Shao M, Zhang J, Wang H. The Role of m6A RNA Methylation in Cancer: Implication for Nature Products Anti-Cancer Research. Front Pharmacol 2022; 13:933332. [PMID: 35784761 PMCID: PMC9243580 DOI: 10.3389/fphar.2022.933332] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/27/2022] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is identified as the most common, abundant and reversible RNA epigenetic modification in messenger RNA (mRNA) and non-coding RNA, especially within eukaryotic messenger RNAs (mRNAs), which post-transcriptionally directs many important processes of RNA. It has also been demonstrated that m6A modification plays a pivotal role in the occurrence and development of tumors by regulating RNA splicing, localization, translation, stabilization and decay. Growing number of studies have indicated that natural products have outstanding anti-cancer effects of their unique advantages of high efficiency and minimal side effects. However, at present, there are very few research articles to study and explore the relationship between natural products and m6A RNA modification in tumorigenesis. m6A is dynamically deposited, removed, and recognized by m6A methyltransferases (METTL3/14, METTL16, WTAP, RBM15/15B, VIRMA, CBLL1, and ZC3H13, called as “writers”), demethylases (FTO and ALKBH5, called as “erasers”), and m6A-specific binding proteins (YTHDF1/2/3, YTHDC1/2, IGH2BP1/2/3, hnRNPs, eIF3, and FMR1, called as “readers”), respectively. In this review, we summarize the biological function of m6A modification, the role of m6A and the related signaling pathway in cancer, such as AKT, NF-kB, MAPK, ERK, Wnt/β-catenin, STAT, p53, Notch signaling pathway, and so on. Furthermore, we reviewed the current research on nature products in anti-tumor, and further to get a better understanding of the anti-tumor mechanism, thus provide an implication for nature products with anti-cancer research by regulating m6A modification in the future.
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Affiliation(s)
- Na Song
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Kai Cui
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Ke Zhang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Jie Yang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Jia Liu
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Zhuang Miao
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Feiyue Zhao
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Hongjing Meng
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Lu Chen
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Chong Chen
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Yushan Li
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Minglong Shao
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Jinghang Zhang
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jinghang Zhang, ; Haijun Wang,
| | - Haijun Wang
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jinghang Zhang, ; Haijun Wang,
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Two zinc finger proteins with functions in m 6A writing interact with HAKAI. Nat Commun 2022; 13:1127. [PMID: 35236848 PMCID: PMC8891334 DOI: 10.1038/s41467-022-28753-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/09/2022] [Indexed: 12/30/2022] Open
Abstract
The methyltransferase complex (m6A writer), which catalyzes the deposition of N6-methyladenosine (m6A) in mRNAs, is highly conserved across most eukaryotic organisms, but its components and interactions between them are still far from fully understood. Here, using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, are discovered as components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA (mRNA adenosine methylase A). Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation and decreased lateral root formation. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ2 is likely the plant equivalent of ZC3H13 (Flacc) of the metazoan m6A-METTL Associated Complex. The components of m6A writer and their interactions are still far from fully understood. Here, the authors identify two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, as components of the Arabidopsis m6A writer complex, and show that hiz2 mutant plants have an 85% reduction in m6A abundance and severe developmental defects.
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75
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Wang S, Lv W, Li T, Zhang S, Wang H, Li X, Wang L, Ma D, Zang Y, Shen J, Xu Y, Wei W. Dynamic regulation and functions of mRNA m6A modification. Cancer Cell Int 2022; 22:48. [PMID: 35093087 PMCID: PMC8800407 DOI: 10.1186/s12935-022-02452-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/03/2022] [Indexed: 12/27/2022] Open
Abstract
AbstractN6-Methyladenosine (m6A), the most abundant internal modification associated with eukaryotic mRNAs, has emerged as a dynamic regulatory mechanism controlling the expression of genes involved in many physiological activities by affecting various steps of mRNA metabolism, including splicing, export, translation, and stability. Here, we review the general role of m6A, highlighting recent advances related to the three major types enzymes that determine the level of m6A modification (i.e., writers, erasers, and readers) and the regulatory mechanism by which m6A influences multiple stages of RNA metabolism. This review clarifies the close connection and interaction between m6A modification and nuclear gene expression, and provides key background information for further studies of its roles in numerous physiological and pathophysiological processes. Among them, perhaps the most eye-catching process is tumorigenesis. Clarifying the molecular mechanism of tumorigenesis, development and metastasis in various tissues of the human body is conducive to curbing out-of-control cell activities from the root and providing a new strategy for human beings to defeat tumors.
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76
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Cai T, Atteh LL, Zhang X, Huang C, Bai M, Ma H, Zhang C, Fu W, Gao L, Lin Y, Meng W. The N6-Methyladenosine Modification and Its Role in mRNA Metabolism and Gastrointestinal Tract Disease. Front Surg 2022; 9:819335. [PMID: 35155557 PMCID: PMC8831730 DOI: 10.3389/fsurg.2022.819335] [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: 11/21/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
The N6-methyladenosine (m6A) modification is the most abundant internal modification of messenger RNA (mRNA) in higher eukaryotes. Under the actions of methyltransferase, demethylase and methyl-binding protein, m6A resulting from RNA methylation becomes dynamic and reversible, similar to that from DNA methylation, and this effect allows the generated mRNA to participate in metabolism processes, such as splicing, transport, translation, and degradation. The most common tumors are those found in the gastrointestinal tract, and research on these tumors has flourished since the discovery of m6A. Overall, further analysis of the mechanism of m6A and its role in tumors may contribute to new ideas for the treatment of tumors. m6A also plays an important role in non-tumor diseases of the gastrointestinal tract. This manuscript reviews the current knowledge of m6A-related proteins, mRNA metabolism and their application in gastrointestinal tract disease.
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Affiliation(s)
- Teng Cai
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Gansu Province Key Laboratory Biotherapy and Regenerative Medicine, Lanzhou, China
| | | | - Xianzhuo Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Chongfei Huang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Mingzhen Bai
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Haidong Ma
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Chao Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Wenkang Fu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Long Gao
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Yanyan Lin
- The Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Institute of Hepatopancreatobiliary Surgery, Lanzhou, China
- Yanyan Lin
| | - Wenbo Meng
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- The Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Institute of Hepatopancreatobiliary Surgery, Lanzhou, China
- *Correspondence: Wenbo Meng
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77
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Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
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78
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Fan C, Ma Y, Chen S, Zhou Q, Jiang H, Zhang J, Wu F. Comprehensive Analysis of the Transcriptome-Wide m6A Methylation Modification Difference in Liver Fibrosis Mice by High-Throughput m6A Sequencing. Front Cell Dev Biol 2021; 9:767051. [PMID: 34869362 PMCID: PMC8635166 DOI: 10.3389/fcell.2021.767051] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/01/2021] [Indexed: 01/01/2023] Open
Abstract
N6-Methyladenosine (m6A), a unique and common mRNA modification method in eukaryotes, is involved in the occurrence and development of many diseases. Liver fibrosis (LF) is a common response to chronic liver injury and may lead to cirrhosis and even liver cancer. However, the involvement of m6A methylation in the development of LF is still unknown. In this study, we performed a systematic evaluation of hepatic genome-wide m6A modification and mRNA expression by m6A-seq and RNA-seq using LF mice. There were 3,315 genes with significant differential m6A levels, of which 2,498 were hypermethylated and 817 hypomethylated. GO and KEGG analyses illustrated that differentially expressed m6A genes were closely correlated with processes such as the endoplasmic reticulum stress response, PPAR signaling pathway and TGF-β signaling pathway. Moreover, a total of 90 genes had both a significant change in the m6A level and mRNA expression shown by joint analysis of m6A-seq and RNA-seq. Hence, the critical elements of m6A modification, including methyltransferase WTAP, demethylases ALKBH5 and binding proteins YTHDF1 were confirmed by RT-qPCR and Western blot. In an additional cell experiment, we also observed that the decreased expression of WTAP induced the development of LF as a result of promoting hepatic stellate cell (HSC) activation. Therefore, this study revealed unique differential m6A methylation patterns in LF mice and suggested that m6A methylation was associated with the occurrence and course of LF to some extent.
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Affiliation(s)
- Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yanzhen Ma
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Sen Chen
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Qiumei Zhou
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Furong Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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79
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Zhang L, Cao R, Li D, Sun Y, Zhang J, Wang X, Khan A, Liu Z, Niu B, Xu J, Xie J. Ethionine-mediated reduction of S-adenosylmethionine is responsible for the neural tube defects in the developing mouse embryo-mediated m6A modification and is involved in neural tube defects via modulating Wnt/β-catenin signaling pathway. Epigenetics Chromatin 2021; 14:52. [PMID: 34863249 PMCID: PMC8645112 DOI: 10.1186/s13072-021-00426-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Neural tube defects (NTDs) remain one of the most life-threatening birth defects affecting infants. Most patients with NTDs eventually develop lifelong disability, which cause significant morbidity and mortality and seriously reduce the quality of life. Our previous study has found that ethionine inhibits cell viability by disrupting the balance between proliferation and apoptosis, and preventing neural stem cells from differentiating into neurons and astrocytes. However, how ethionine participates in the pathogenesis of neural tube development through N6-methyladenosine (m6A) modification remains unknown. This study aims to investigate METTL3- and ALKBH5-mediated m6A modification function and mechanism in NTDs. Herein, our results demonstrate that SAM play not only a compensatory role, it also leads to changes of m6A modification in neural tube development and regulation. Additionally, these data implicate that METTL3 is enriched in HT-22 cells, and METTL3 knockdown reduces cell proliferation and increases apoptosis through suppressing Wnt/β-catenin signaling pathway. Significantly, overexpression of ALKBH5 can only inhibit cell proliferation, but cannot promote cell apoptosis. This research reveals an important role of SAM in development of NTDs, providing a good theoretical basis for further research on NTDs. This finding represents a novel epigenetic mechanism underlying that the m6A modification has profound and lasting implications for neural tube development.
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Affiliation(s)
- Li Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Department of Hepatobiliary and Pancreatic Surgery, First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Institute of Liver Diseases and Organ Transplantation, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Rui Cao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Biology Institute of Shanxi, Taiyuan, 030001, Shanxi, China
| | - Dandan Li
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Yuqing Sun
- Department of Hepatobiliary and Pancreatic Surgery, First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Institute of Liver Diseases and Organ Transplantation, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Xiuwei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Ajab Khan
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Bo Niu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Jun Xu
- Department of Hepatobiliary and Pancreatic Surgery, First Clinical Medical College, Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,Institute of Liver Diseases and Organ Transplantation, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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80
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Guo J, Zheng J, Zhang H, Tong J. RNA m6A methylation regulators in ovarian cancer. Cancer Cell Int 2021; 21:609. [PMID: 34794452 PMCID: PMC8600856 DOI: 10.1186/s12935-021-02318-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/05/2021] [Indexed: 12/19/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification of mammalian mRNAs and plays a vital role in many diseases, especially tumours. In recent years, m6A has become the topic of intense discussion in epigenetics. M6A modification is dynamically regulated by methyltransferases, demethylases and RNA-binding proteins. Ovarian cancer (OC) is a common but highly fatal malignancy in female. Increasing evidence shows that changes in m6A levels and the dysregulation of m6A regulators are associated with the occurrence, development or prognosis of OC. In this review, the latest studies on m6A and its regulators in OC have been summarized, and we focus on the key role of m6A modification in the development and progression of OC. Additionally, we also discuss the potential use of m6A modification and its regulators in the diagnosis and treatment of OC.
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Affiliation(s)
- Jialu Guo
- Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang Province, People's Republic of China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), 310008, Hangzhou, Zhejiang Province, People's Republic of China
| | - Jianfeng Zheng
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), 310008, Hangzhou, Zhejiang Province, People's Republic of China.,Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, 310008, Hangzhou, Zhejiang Province, People's Republic of China
| | - Huizhi Zhang
- Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang Province, People's Republic of China
| | - Jinyi Tong
- Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang Province, People's Republic of China. .,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), 310008, Hangzhou, Zhejiang Province, People's Republic of China.
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81
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Ha N, Ding N, Hong R, Liu R, Roca X, Luo Y, Duan X, Wang X, Ni P, Wu H, Zhang LF, Chen L. The lupus autoantigen La/Ssb is an Xist-binding protein involved in Xist folding and cloud formation. Nucleic Acids Res 2021; 49:11596-11613. [PMID: 34723322 PMCID: PMC8599922 DOI: 10.1093/nar/gkab1003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/25/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Using the programmable RNA-sequence binding domain of the Pumilio protein, we FLAG-tagged Xist (inactivated X chromosome specific transcript) in live mouse cells. Affinity pulldown coupled to mass spectrometry was employed to identify a list of 138 candidate Xist-binding proteins, from which, Ssb (also known as the lupus autoantigen La) was validated as a protein functionally critical for X chromosome inactivation (XCI). Extensive XCI defects were detected in Ssb knockdown cells, including chromatin compaction, death of female mouse embryonic stem cells during in vitro differentiation and chromosome-wide monoallelic gene expression pattern. Live-cell imaging of Xist RNA reveals the defining XCI defect: Xist cloud formation. Ssb is a ubiquitous and versatile RNA-binding protein with RNA chaperone and RNA helicase activities. Functional dissection of Ssb shows that the RNA chaperone domain plays critical roles in XCI. In Ssb knockdown cells, Xist transcripts are unstable and misfolded. These results show that Ssb is critically involved in XCI, possibly as a protein regulating the in-cell structure of Xist.
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Affiliation(s)
- Norbert Ha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Nan Ding
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ru Hong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Rubing Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yingyuan Luo
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaowei Duan
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiao Wang
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Peiling Ni
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiyang Wu
- TCRCure Biological Technology Co Ltd., Guangdong, China
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- TCRCure Biological Technology Co Ltd., Guangdong, China
| | - Lingyi Chen
- Institute of Translational Medicine, Tianjin Union Medical Center, State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, Tianjin 300071, China
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82
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Șelaru A, Costache M, Dinescu S. Epitranscriptomic signatures in stem cell differentiation to the neuronal lineage. RNA Biol 2021; 18:51-60. [PMID: 34582322 PMCID: PMC8677044 DOI: 10.1080/15476286.2021.1985348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022] Open
Abstract
Considered to be a field that is continuously growing, epitranscriptomics analyzes the modifications that occur in RNA transcripts and their downstream effects. As epigenetic modifications found in DNA and histones exhibit specific roles on various biological processes, also epitranscriptomic marks control gene expression patterns that are crucial for proper cell proliferation, differentiation and tissue development. Thus, various epitranscriptomic signatures have been identified to play specific roles during stem cell differentiation towards the neuronal and glial lineages, axonal guidance, synaptic plasticity, thus leading to the development of the mature brain tissue. Here we describe in-depth molecular mechanism underlying the most important RNA modifications with emerging roles in the nervous system.
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Affiliation(s)
- Aida Șelaru
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, Bucharest, Romania
| | - Sorina Dinescu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, Bucharest, Romania
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83
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Wu S, Li XF, Wu YY, Yin SQ, Huang C, Li J. N6 -Methyladenosine and Rheumatoid Arthritis: A Comprehensive Review. Front Immunol 2021; 12:731842. [PMID: 34630412 PMCID: PMC8498590 DOI: 10.3389/fimmu.2021.731842] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/09/2021] [Indexed: 12/17/2022] Open
Abstract
Rheumatoid arthritis (RA), one of the most common autoimmune diseases, is characterized by immune cell infiltration, fibroblast-like synovial cell hyperproliferation, and cartilage and bone destruction. To date, numerous studies have demonstrated that immune cells are one of the key targets for the treatment of RA. N6-methyladenosine (m6A) is the most common internal modification to eukaryotic mRNA, which is involved in the splicing, stability, export, and degradation of RNA metabolism. m6A methylated-related genes are divided into writers, erasers, and readers, and they are critical for the regulation of cell life. They play a significant role in various biological processes, such as virus replication and cell differentiation by controlling gene expression. Furthermore, a growing number of studies have indicated that m6A is associated with the occurrence of numerous diseases, such as lung cancer, bladder cancer, gastric cancer, acute myeloid leukemia, and hepatocellular carcinoma. In this review, we summarize the history of m6A research and recent progress on RA research concerning m6A enzymes. The relationship between m6A enzymes, immune cells, and RA suggests that m6A modification offers evidence for the pathogenesis of RA, which will help in the development of new therapies for RA.
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Affiliation(s)
- Sha Wu
- Anhui Institute of Innovative Drugs, The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Xiao-Feng Li
- Anhui Institute of Innovative Drugs, The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China.,Postdoctoral Station of Clinical Medicine of Anhui Medical University, Hefei, China
| | - Yuan-Yuan Wu
- Anhui Institute of Innovative Drugs, The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Su-Qin Yin
- Anhui Institute of Innovative Drugs, The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Cheng Huang
- Anhui Institute of Innovative Drugs, The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jun Li
- Anhui Institute of Innovative Drugs, The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
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84
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RNA Modifications and Epigenetics in Modulation of Lung Cancer and Pulmonary Diseases. Int J Mol Sci 2021; 22:ijms221910592. [PMID: 34638933 PMCID: PMC8508636 DOI: 10.3390/ijms221910592] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide, and its tumorigenesis involves the accumulation of genetic and epigenetic events in the respiratory epithelium. Epigenetic modifications, such as DNA methylation, RNA modification, and histone modifications, have been widely reported to play an important role in lung cancer development and in other pulmonary diseases. Whereas the functionality of DNA and chromatin modifications referred to as epigenetics is widely characterized, various modifications of RNA nucleotides have recently come into prominence as functionally important. N6-methyladosine (m6A) is the most prevalent internal modification in mRNAs, and its machinery of writers, erasers, and readers is well-characterized. However, several other nucleotide modifications of mRNAs and various noncoding RNAs have also been shown to play an important role in the regulation of biological processes and pathology. Such epitranscriptomic modifications play an important role in regulating various aspects of RNA metabolism, including transcription, translation, splicing, and stability. The dysregulation of epitranscriptomic machinery has been implicated in the pathological processes associated with carcinogenesis including uncontrolled cell proliferation, migration, invasion, and epithelial-mesenchymal transition. In recent years, with the advancement of RNA sequencing technology, high-resolution maps of different modifications in various tissues, organs, or disease models are being constantly reported at a dramatic speed. This facilitates further understanding of the relationship between disease development and epitranscriptomics, shedding light on new therapeutic possibilities. In this review, we summarize the basic information on RNA modifications, including m6A, m1A, m5C, m7G, pseudouridine, and A-to-I editing. We then demonstrate their relation to different kinds of lung diseases, especially lung cancer. By comparing the different roles RNA modifications play in the development processes of different diseases, this review may provide some new insights and offer a better understanding of RNA epigenetics and its involvement in pulmonary diseases.
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85
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Horiuchi K, Kawamura T, Hamakubo T. Wilms' Tumor 1-Associating Protein complex regulates alternative splicing and polyadenylation at potential G-quadruplex-forming splice site sequences. J Biol Chem 2021; 297:101248. [PMID: 34582888 PMCID: PMC8605363 DOI: 10.1016/j.jbc.2021.101248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/14/2022] Open
Abstract
Wilms’ tumor 1-associating protein (WTAP) is a core component of the N6-methyladenosine (m6A)-methyltransferase complex, along with VIRMA, CBLL1, ZC3H13 (KIAA0853), RBM15/15B, and METTL3/14, which generate m6A, a key RNA modification that affects various processes of RNA metabolism. WTAP also interacts with splicing factors; however, despite strong evidence suggesting a role of Drosophila WTAP homolog fl(2)d in alternative splicing (AS), its role in splicing regulation in mammalian cells remains elusive. Here we demonstrate using RNAi coupled with RNA-seq that WTAP, VIRMA, CBLL1, and ZC3H13 modulate AS, promoting exon skipping and intron retention in AS events that involve short introns/exons with higher GC content and introns with weaker polypyrimidine-tract and branch points. Further analysis of GC-rich sequences involved in AS events regulated by WTAP, together with minigene assay analysis, revealed potential G-quadruplex formation at splice sites where WTAP has an inhibitory effect. We also found that several AS events occur in the last exon of one isoform of MSL1 and WTAP, leading to competition for polyadenylation. Proteomic analysis also suggested that WTAP/CBLL1 interaction promotes recruitment of the 3′-end processing complex. Taken together, our results indicate that the WTAP complex regulates AS and alternative polyadenylation via inhibitory mechanisms in GC-rich sequences.
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Affiliation(s)
- Keiko Horiuchi
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-0011, Japan.
| | - Takeshi Kawamura
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-0011, Japan.
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86
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Ghazi T, Nagiah S, Chuturgoon AA. Fusaric acid induces hepatic global m6A RNA methylation and differential expression of m6A regulatory genes in vivo - a pilot study. Epigenetics 2021; 17:695-703. [PMID: 34517792 DOI: 10.1080/15592294.2021.1975937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant epitranscriptomic mark that regulates gene expression to execute cellular developmental programmes and environmental adaptation. Fusaric acid (FA) is a mycotoxin that contaminates agricultural foods and exerts toxicity in humans and animals; however, its epitranscriptomic effects are unclear. We investigated the effect of FA on global m6A RNA methylation and mRNA expression levels of key m6A regulatory genes in C57BL/6 mouse livers. C57BL/6 mice (n = 6/group) were orally administered 0.1 M phosphate-buffered saline (PBS) or 50 mg/kg FA. Mice were euthanized 24 h after oral administration, livers were harvested, and RNA was isolated. RNA samples were assayed for global m6A levels using an m6A RNA Methylation Quantification Kit. The mRNA expression of m6A regulators i.e. writers, erasers, and readers were measured by qRT-PCR. FA increased global m6A RNA methylation (p < 0.0001) in mouse livers. FA increased the expression of METTL3 (p = 0.0143) and METTL14 (p = 0.0281), and decreased the expression of FTO (p = 0.0036) and ALKBH5 (p = 0.0035). The expression of YTHDF2 (p = 0.0007), YTHDF3 (p = 0.0061), and YTHDC2 (p = 0.0258) were increased by FA in mouse livers. This study shows that the liver m6A epitranscriptome can be modified by FA exposure in an in vivo model and can be useful for identifying the molecular mechanisms whereby m6A RNA modifications influence the toxicological outcomes of FA exposure.
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Affiliation(s)
- Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Savania Nagiah
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban, South Africa
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87
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Zhou H, Yin K, Zhang Y, Tian J, Wang S. The RNA m6A writer METTL14 in cancers: Roles, structures, and applications. Biochim Biophys Acta Rev Cancer 2021; 1876:188609. [PMID: 34375716 DOI: 10.1016/j.bbcan.2021.188609] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant and diverse epigenetic modification of mRNAs in eukaryotes, and it regulates biological metabolism, cell differentiation and cycles, and responses to heat shock stress, cancers and other diseases. RNA methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14) and other proteins possessing methyltransferase (MTase) capability including Wilms tumor 1-associated protein (WTAP), RNA-binding motif protein 15(RBM15), KIAA 1429 and zinc finger CCCH-type containing 13 (ZC3H13) constitute the m6A writer complex. Although METTL3 is the catalytic subunit, its activity is strongly dependent on METTL14, which is crucial in maintaining complex integrity and recognizing special RNA substrates. Currently, the roles of m6A modification in cancers are being extensively reviewed. The critical functions of METTL14 in the occurrence and development of a variety of cancers as well as the potential targeting of METTL14 as a cancer treatment have not yet been highlighted. Therefore, in this review, we summarize the m6A modification and focus on the structure and functions of METTL14 as well as its roles in oncogenesis, metastasis progression, treatment and prognosis in cancer.
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Affiliation(s)
- Huimin Zhou
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Kai Yin
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Yue Zhang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Jie Tian
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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88
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Liang RH, Zhu NX, Hou Q, Wu LF. Role of m6A methylation in occurrence and progression of digestive system malignancies. Shijie Huaren Xiaohua Zazhi 2021; 29:747-757. [DOI: 10.11569/wcjd.v29.i14.747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is the most common modification in higher eukaryotic messenger RNA (mRNA), which is closely related to the mRNA processing, nuclear output, translation, and degradation. M6A modification is regulated by methyltransferase and demethylase dynamically and reversibly. M6A plays an essential role in tumors progression by regulating epigenetic modification of tumor suppressor genes and oncogenes. In recent years, more and more studies have shown that m6A is related to the occurrence and development of digestive system malignant tumors and may serve as a novel potential biomarker for the diagnosis and prognosis of digestive cancer. This article reviews the latest progress in the research of m6A in digestive system malignant tumors.
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Affiliation(s)
- Rui-Huang Liang
- Department of Gastroenterology, the 2nd Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Nan-Xing Zhu
- Department of Gastroenterology, the 2nd Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Qin Hou
- Department of Gastroenterology, the 2nd Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Ling-Fei Wu
- Department of Gastroenterology, the 2nd Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
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89
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EBV downregulates the m 6A "writer" WTAP in EBV-associated gastric carcinoma. Virus Res 2021; 304:198510. [PMID: 34329695 DOI: 10.1016/j.virusres.2021.198510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022]
Abstract
Epstein-Barr virus-associated gastric carcinoma (EBVaGC) is characterized by the clonal growth of EBV-infected stomach epithelial cells. It has been reported that N6-methyladenosine (m6A) methylation can regulate the splicing, expression, decay and translation of mRNAs. Wilms' tumor 1-associating protein (WTAP) is an m6A "writer" with methyltransferase activity. An m6A RNA methylation quantification kit and immunofluorescence (IF) showed that the m6A total RNA methylation level of the Epstein-Barr virus-negative gastric carcinoma (EBVnGC) cell line (SGC7901) was higher than that in the EBVaGC cell line (GT38). To investigate the underlying mechanism of the downregulated expression of m6A RNA methylation, we analyzed the expression of WTAP. The results showed that the expression of WTAP protein in EBVaGC cell lines was significantly lower than that in EBVnGC cell lines according to western blotting and IF. Through plasmid overexpression and RNA interference technology, we further found that EBV-encoded small RNA1 (EBER1) could downregulate WTAP expression by activating the NF-κB signaling pathway. In addition, WTAP could increase proliferation and inhibit migration in gastric carcinoma cell lines. In summary, EBER1 of EBV potentially regulated WTAP by affecting the NF-κB signaling pathway and WTAP further affected cell proliferation and migration.
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90
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Srinivas KP, Depledge DP, Abebe JS, Rice SA, Mohr I, Wilson AC. Widespread remodeling of the m 6A RNA-modification landscape by a viral regulator of RNA processing and export. Proc Natl Acad Sci U S A 2021; 118:e2104805118. [PMID: 34282019 PMCID: PMC8325250 DOI: 10.1073/pnas.2104805118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal messenger RNA (mRNA) modification, contributing to the processing, stability, and function of methylated RNAs. Methylation occurs in the nucleus during pre-mRNA synthesis and requires a core methyltransferase complex consisting of METTL3, METTL14, and WTAP. During herpes simplex virus (HSV-1) infection, cellular gene expression is profoundly suppressed, allowing the virus to monopolize the host transcription and translation apparatus and antagonize antiviral responses. The extent to which HSV-1 uses or manipulates the m6A pathway is not known. Here, we show that, in primary fibroblasts, HSV-1 orchestrates a striking redistribution of the nuclear m6A machinery that progresses through the infection cycle. METTL3 and METTL14 are dispersed into the cytoplasm, whereas WTAP remains nuclear. Other regulatory subunits of the methyltransferase complex, along with the nuclear m6A-modified RNA binding protein YTHDC1 and nuclear demethylase ALKBH5, are similarly redistributed. These changes require ICP27, a viral regulator of host mRNA processing that mediates the nucleocytoplasmic export of viral late mRNAs. Viral gene expression is initially reduced by small interfering RNA (siRNA)-mediated inactivation of the m6A methyltransferase but becomes less impacted as the infection advances. Redistribution of the nuclear m6A machinery is accompanied by a wide-scale reduction in the installation of m6A and other RNA modifications on both host and viral mRNAs. These results reveal a far-reaching mechanism by which HSV-1 subverts host gene expression to favor viral replication.
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Affiliation(s)
| | - Daniel P Depledge
- Department of Medicine, New York University Grossman School of Medicine, New York University, New York, NY 10016
| | - Jonathan S Abebe
- Department of Medicine, New York University Grossman School of Medicine, New York University, New York, NY 10016
| | - Stephen A Rice
- Department of Microbiology, University of Minnesota Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Ian Mohr
- Department of Microbiology, New York University Grossman School of Medicine, New York University, New York, NY 10016
| | - Angus C Wilson
- Department of Microbiology, New York University Grossman School of Medicine, New York University, New York, NY 10016;
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91
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Wu J, Guo X, Wen Y, Huang S, Yuan X, Tang L, Sun H. N6-Methyladenosine Modification Opens a New Chapter in Circular RNA Biology. Front Cell Dev Biol 2021; 9:709299. [PMID: 34368159 PMCID: PMC8342999 DOI: 10.3389/fcell.2021.709299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
As the most abundant internal modification in eukaryotic cells, N6-methyladenosine (m6A) in mRNA has shown widespread regulatory roles in a variety of physiological processes and disease progressions. Circular RNAs (circRNAs) are a class of covalently closed circular RNA molecules and play an essential role in the pathogenesis of various diseases. Recently, accumulating evidence has shown that m6A modification is widely existed in circRNAs and found its key biological functions in regulating circRNA metabolism, including biogenesis, translation, degradation and cellular localization. Through regulating circRNAs, studies have shown the important roles of m6A modification in circRNAs during immunity and multiple diseases, which represents a new layer of control in physiological processes and disease progressions. In this review, we focused on the roles played by m6A in circRNA metabolism, summarized the regulatory mechanisms of m6A-modified circRNAs in immunity and diseases, and discussed the current challenges to study m6A modification in circRNAs and the possible future directions, providing a comprehensive insight into understanding m6A modification of circRNAs in RNA epigenetics.
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Affiliation(s)
- Jun Wu
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, China.,College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Xin Guo
- Laboratory of Basic Medicine, The General Hospital of Western Theater Command, Chengdu, China
| | - Yi Wen
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, China
| | - Shangqing Huang
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, China.,College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Xiaohui Yuan
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, China.,College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Lijun Tang
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, China.,College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Hongyu Sun
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, China.,College of Medicine, Southwest Jiaotong University, Chengdu, China.,Laboratory of Basic Medicine, The General Hospital of Western Theater Command, Chengdu, China
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92
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Zhang W, Qian Y, Jia G. The detection and functions of RNA modification m 6A based on m 6A writers and erasers. J Biol Chem 2021; 297:100973. [PMID: 34280435 PMCID: PMC8350415 DOI: 10.1016/j.jbc.2021.100973] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) is the most frequent chemical modification in eukaryotic mRNA and is known to participate in a variety of physiological processes, including cancer progression and viral infection. The reversible and dynamic m6A modification is installed by m6A methyltransferase (writer) enzymes and erased by m6A demethylase (eraser) enzymes. m6A modification recognized by m6A binding proteins (readers) regulates RNA processing and metabolism, leading to downstream biological effects such as promotion of stability and translation or increased degradation. The m6A writers and erasers determine the abundance of m6A modifications and play decisive roles in its distribution and function. In this review, we focused on m6A writers and erasers and present an overview on their known functions and enzymatic molecular mechanisms, showing how they recognize substrates and install or remove m6A modifications. We also summarize the current applications of m6A writers and erasers for m6A detection and highlight the merits and drawbacks of these available methods. Lastly, we describe the biological functions of m6A in cancers and viral infection based on research of m6A writers and erasers and introduce new assays for m6A functionality via programmable m6A editing tools.
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Affiliation(s)
- Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yang Qian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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93
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Du K, Zhang Z, Zeng Z, Tang J, Lee T, Sun T. Distinct roles of Fto and Mettl3 in controlling development of the cerebral cortex through transcriptional and translational regulations. Cell Death Dis 2021; 12:700. [PMID: 34262022 PMCID: PMC8280107 DOI: 10.1038/s41419-021-03992-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022]
Abstract
Proper development of the mammalian cerebral cortex relies on precise gene expression regulation, which is controlled by genetic, epigenetic, and epitranscriptomic factors. Here we generate RNA demethylase Fto and methyltransferase Mettl3 cortical-specific conditional knockout mice, and detect severe brain defects caused by Mettl3 deletion but not Fto knockout. Transcriptomic profiles using RNA sequencing indicate that knockout of Mettl3 causes a more dramatic alteration on gene transcription than that of Fto. Interestingly, we conduct ribosome profiling sequencing, and find that knockout of Mettl3 leads to a more severe disruption of translational regulation of mRNAs than deletion of Fto and results in altered translation of crucial genes in cortical radial glial cells and intermediate progenitors. Moreover, Mettl3 deletion causes elevated translation of a significant number of mRNAs, in particular major components in m6A methylation. Our findings indicate distinct functions of Mettl3 and Fto in brain development, and uncover a profound role of Mettl3 in regulating translation of major mRNAs that control proper cortical development.
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Affiliation(s)
- Kunzhao Du
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Zhen Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zeng
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Jinling Tang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, New York, NY, USA
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.
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94
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Methyltransferase-like 3 Modulates Severe Acute Respiratory Syndrome Coronavirus-2 RNA N6-Methyladenosine Modification and Replication. mBio 2021; 12:e0106721. [PMID: 34225491 PMCID: PMC8437041 DOI: 10.1128/mbio.01067-21] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an ongoing global public crisis. Although viral RNA modification has been reported based on the transcriptome architecture, the types and functions of RNA modification are still unknown. In this study, we evaluated the roles of RNA N6-methyladenosine (m6A) modification in SARS-CoV-2. Our methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and Nanopore direct RNA sequencing (DRS) analysis showed that SARS-CoV-2 RNA contained m6A modification. Moreover, SARS-CoV-2 infection not only increased the expression of methyltransferase-like 3 (METTL3) but also altered its distribution. Modification of METTL3 expression by short hairpin RNA or plasmid transfection for knockdown or overexpression, respectively, affected viral replication. Furthermore, the viral key protein RdRp interacted with METTL3, and METTL3 was distributed in both the nucleus and cytoplasm in the presence of RdRp. RdRp appeared to modulate the sumoylation and ubiquitination of METTL3 via an unknown mechanism. Taken together, our findings demonstrated that the host m6A modification complex interacted with viral proteins to modulate SARS-CoV-2 replication.
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95
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Feng ZY, Wang T, Su X, Guo S. Identification of the m 6A RNA Methylation Regulators WTAP as a Novel Prognostic Biomarker and Genomic Alterations in Cutaneous Melanoma. Front Mol Biosci 2021; 8:665222. [PMID: 34291082 PMCID: PMC8287526 DOI: 10.3389/fmolb.2021.665222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/22/2021] [Indexed: 02/03/2023] Open
Abstract
Background: The purpose of our research was to establish a gene signature and determine the prognostic value of m6A methylation regulators in cutaneous melanoma and WTAP as a protective gene in cutaneous melanoma prognosis, we also evaluated gene mutations in cutaneous melanoma. Methods: We downloaded the RNA-seq transcriptome data and the clinical information for cutaneous melanoma patients from the GTEx and TCGA databases. Consensus clustering analysis was applied to divide the samples into two groups. Then the least absolute shrinkage and selection operator (LASSO) analyses were conducted to construct a risk signature, and we use external and internal datasets to verify its predictive value. We further searched the cBioPortal tools to detect genomic alterations and WTAP mutations. Finally, WTAP was further identified as a prognostic factor, and the related mechanisms mediated by WTAP were predicted by gene set enrichment analysis (GSEA). Experimental validations and have been further carried out. Results: Notably, m6A RNA methylation regulators play significant roles in tumorigenesis and development. In total, we selected three subtypes of cutaneous melanoma according to consensus clustering of the m6A RNA methylation regulators, and the stage of cutaneous melanoma was proven to be related to the subtypes. The Cox regression and LASSO analyses built a risk signature including ELF3, ZC3H13 and WTAP. The prognostic value of the risk signature in internal and external datasets have been proven then. The whole-genome and selected gene WTAP mutations were further explored. WTAP as a single prognostic factor was also explored and found to serve as an independent protective prognostic factor. Conclusions: Our study constructed a stable risk signature composed of m6A RNA methylation regulators in cutaneous melanoma. Moreover, WTAP was identified as a valuable prognostic factor and potential molecular target for cutaneous melanoma treatment.
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Affiliation(s)
- Zi-Yi Feng
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ting Wang
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xin Su
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Shu Guo
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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96
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Jia GX, Lin Z, Yan RG, Wang GW, Zhang XN, Li C, Tong MH, Yang QE. WTAP Function in Sertoli Cells Is Essential for Sustaining the Spermatogonial Stem Cell Niche. Stem Cell Reports 2021; 15:968-982. [PMID: 33053361 PMCID: PMC7566211 DOI: 10.1016/j.stemcr.2020.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
Sertoli cells are the major component of the spermatogonial stem cell (SSC) niche; however, regulatory mechanisms in Sertoli cells that dictate SSC fate decisions remain largely unknown. Here we revealed features of the N6-methyladenosine (m6A) mRNA modification in Sertoli cells and demonstrated the functions of WTAP, the key subunit of the m6A methyltransferase complex in spermatogenesis. m6A-sequencing analysis identified 21,909 m6A sites from 15,365 putative m6A-enriched transcripts within 6,122 genes, including many Sertoli cell-specific genes. Conditional deletion of Wtap in Sertoli cells resulted in sterility and the progressive loss of the SSC population. RNA sequencing and ribosome nascent-chain complex-bound mRNA sequencing analyses suggested that alternative splicing events of transcripts encoding SSC niche factors were sharply altered and translation of these transcripts were severely dysregulated by Wtap deletion. Collectively, this study uncovers a novel regulatory mechanism of the SSC niche and provide insights into molecular interactions between stem cells and their cognate niches in mammals. WTAP is highly expressed in Sertoli cell and is essential in spermatogenesis Wtap knockout in Sertoli cell causes defective spermatogonial stem cell maintenance WTAP regulates transcription and translation of m6A-enriched genes in Sertoli cell
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Affiliation(s)
- Gong-Xue Jia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Zhen Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Rong-Ge Yan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Guo-Wen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Na Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cen Li
- Qinghai Provincial Key Laboratory of Tibetan Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Ming-Han Tong
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China; University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.
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97
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Bawankar P, Lence T, Paolantoni C, Haussmann IU, Kazlauskiene M, Jacob D, Heidelberger JB, Richter FM, Nallasivan MP, Morin V, Kreim N, Beli P, Helm M, Jinek M, Soller M, Roignant JY. Hakai is required for stabilization of core components of the m 6A mRNA methylation machinery. Nat Commun 2021; 12:3778. [PMID: 34145251 PMCID: PMC8213727 DOI: 10.1038/s41467-021-23892-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/17/2021] [Indexed: 11/10/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on mRNA which influences most steps of mRNA metabolism and is involved in several biological functions. The E3 ubiquitin ligase Hakai was previously found in complex with components of the m6A methylation machinery in plants and mammalian cells but its precise function remained to be investigated. Here we show that Hakai is a conserved component of the methyltransferase complex in Drosophila and human cells. In Drosophila, its depletion results in reduced m6A levels and altered m6A-dependent functions including sex determination. We show that its ubiquitination domain is required for dimerization and interaction with other members of the m6A machinery, while its catalytic activity is dispensable. Finally, we demonstrate that the loss of Hakai destabilizes several subunits of the methyltransferase complex, resulting in impaired m6A deposition. Our work adds functional and molecular insights into the mechanism of the m6A mRNA writer complex. The E3 ligase Hakai can interact with the m6A methylation machinery but its function is still unclear. Here, the authors show that Hakai is a conserved component of the m6A methyltransferase complex and provide functional and molecular insights into its role in regulating m6A levels in Drosophila.
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Affiliation(s)
- Praveen Bawankar
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK.,Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City University, Birmingham, UK
| | | | - Dominik Jacob
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | - Florian M Richter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Mohanakarthik P Nallasivan
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Violeta Morin
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics core facility, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK. .,Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany. .,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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98
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Liu C, Yang Z, Li R, Wu Y, Chi M, Gao S, Sun X, Meng X, Wang B. Potential roles of N6-methyladenosine (m6A) in immune cells. J Transl Med 2021; 19:251. [PMID: 34103054 PMCID: PMC8186046 DOI: 10.1186/s12967-021-02918-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/29/2021] [Indexed: 12/20/2022] Open
Abstract
N6-methyl-adenosine (m6A) is one of the most common internal modifications on RNA molecules present in mammalian cells. Deregulation of m6A modification has been recently implicated in many types of human diseases. Therefore, m6A modification has become a research hotspot for its potential therapeutic applications in the treatment of various diseases. The immune system mostly involves different types of immune cells to provide the first line of defense against infections. The immunoregulatory network that orchestrate the immune responses to new pathogens plays a pivotal role in the development of the disease. And m6A modification has been demonstrated to be a major post-transcriptional regulator of immune responses in cells. In this review, we summarize the participants involved in m6A regulation and try to reveal how m6A modification affects the immune responses via changing the immunoregulatory networks.
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Affiliation(s)
- Chang Liu
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, No. 155 NanJing North Road, Shenyang, China
| | - Zhe Yang
- College of Life Science, Liaoning University, 66 Chongshan Road, Shenyang, 110036, People's Republic of China
| | - Rong Li
- College of Life Science, Liaoning University, 66 Chongshan Road, Shenyang, 110036, People's Republic of China
| | - Yanju Wu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Ming Chi
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Shuting Gao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xun Sun
- Department of Immunology, College of Basic Medical Sciences of China Medical University, , No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xin Meng
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Biao Wang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China.
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99
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Loss of WTAP Impairs Early Parthenogenetic Embryo Development. Animals (Basel) 2021; 11:ani11061675. [PMID: 34199793 PMCID: PMC8229322 DOI: 10.3390/ani11061675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
m6A is one of the most common and abundant modifications of RNA molecules present in eukaryotes. The methyltransferase complex, consisting of methyltransferase-like 3 (METTL3), METTL14, and WTAP, is responsible for the m6A modification of RNA. WTAP was identified as an mRNA splicing regulator. Its role as a regulatory subunit of the m6A methyltransferase complex in embryonic development remains largely unknown. To investigate the role of WTAP in porcine early embryonic development, si-WTAP was microinjected into porcine parthenogenetic zygotes. WTAP knockdown significantly reduced the blastocyst rate and global m6A levels, but did not affect the cleavage rate. Betaine was supplemented into the in vitro culture (IVC) to increase the m6A levels. Betaine significantly increased the global m6A levels but did not affect the blastocyst rate. Furthermore, the pluripotency genes, including OCT4, SOX2, and NANOG, were downregulated following WTAP knockdown. The apoptotic genes BAX and CASPASE 3 were upregulated, while the anti-apoptotic gene BCL2 was downregulated in WTAP knockdown blastocysts. TUNEL staining revealed that the number of apoptotic cells was significantly increased following WTAP knockdown. Our study indicated that WTAP has an indispensable role in porcine early embryonic development.
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100
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Han X, Liu J, Cheng G, Cui S. Gene Signatures and Prognostic Values of m6A RNA Methylation Regulators in Ovarian Cancer. Cancer Control 2021; 27:1073274820960460. [PMID: 32951457 PMCID: PMC7791456 DOI: 10.1177/1073274820960460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most common form of mRNA modification under the field of "RNA epigenetics." However, its role in ovarian cancer (OC) development is poorly understood. In the current study, we aimed to identify gene signatures and prognostic values of m6A RNA methylation regulators. METHOD Specifically, we downloaded Mutations and Copy number variant (CNV) data from the TCGA database for 579 OC patients, then analyzed gene expression and prognosis value using integrative bioinformatics. Thereafter, we verified the related biological processes of Wilms' tumor 1-associating protein (WTAP) gene using Gene set enrichment analysis (GSEA). RESULTS Results showed that almost all ovarian cancer patients (99.31%) have CNVs with at least 1 m6A regulatory gene, whereas 83.76% of cases exhibited concurrence of CNVs in more than 4 m6A regulatory genes. Additionally, alteration of m6A regulators was associated with historical grade, whereas integrative bioinformatics and Cox multivariate model analysis revealed a significant correlation between high WTAP expression and worse ovarian cancer outcomes. Moreover, GSEA revealed that high WTAP expression was associated with cell cycle regulation and MYC targets. CONCLUSION Overall, our findings demonstrate the significance of high-frequency genetic alterations of m6A RNA methylation regulators and WTAP's poor prognosis value in OC. These findings provide valuable insights into the role of m6A methylation in OC, and will be vital in guiding development of novel treatment therapies.
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Affiliation(s)
- Xiao Han
- Department of Obstetrics and Gynecology, 117977The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Liu
- Department of Internal Medicine, 117977The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, China
| | - Guomei Cheng
- Department of Obstetrics and Gynecology, 117977The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shihong Cui
- Department of Obstetrics and Gynecology, 117977The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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