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Bortoletto E, Rosani U. Bioinformatics for Inosine: Tools and Approaches to Trace This Elusive RNA Modification. Genes (Basel) 2024; 15:996. [PMID: 39202357 PMCID: PMC11353476 DOI: 10.3390/genes15080996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 09/03/2024] Open
Abstract
Inosine is a nucleotide resulting from the deamination of adenosine in RNA. This chemical modification process, known as RNA editing, is typically mediated by a family of double-stranded RNA binding proteins named Adenosine Deaminase Acting on dsRNA (ADAR). While the presence of ADAR orthologs has been traced throughout the evolution of metazoans, the existence and extension of RNA editing have been characterized in a more limited number of animals so far. Undoubtedly, ADAR-mediated RNA editing plays a vital role in physiology, organismal development and disease, making the understanding of the evolutionary conservation of this phenomenon pivotal to a deep characterization of relevant biological processes. However, the lack of direct high-throughput methods to reveal RNA modifications at single nucleotide resolution limited an extended investigation of RNA editing. Nowadays, these methods have been developed, and appropriate bioinformatic pipelines are required to fully exploit this data, which can complement existing approaches to detect ADAR editing. Here, we review the current literature on the "bioinformatics for inosine" subject and we discuss future research avenues in the field.
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Affiliation(s)
| | - Umberto Rosani
- Department of Biology, University of Padova, 35131 Padova, Italy;
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Ma L, Zhou X, Yao S, Zhang X, Mao J, Vona B, Fan L, Lou S, Li D, Wang L, Pan Y. METTL3-dependent m 6A modification of PSEN1 mRNA regulates craniofacial development through the Wnt/β-catenin signaling pathway. Cell Death Dis 2024; 15:229. [PMID: 38509077 PMCID: PMC10954657 DOI: 10.1038/s41419-024-06606-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Craniofacial malformations, often associated with syndromes, are prevalent birth defects. Emerging evidence underscores the importance of m6A modifications in various bioprocesses such as stem cell differentiation, tissue development, and tumorigenesis. Here, in vivo, experiments with zebrafish models revealed that mettl3-knockdown embryos at 144 h postfertilization exhibited aberrant craniofacial features, including altered mouth opening, jaw dimensions, ethmoid plate, tooth formation and hypoactive behavior. Similarly, low METTL3 expression inhibited the proliferation and migration of BMSCs, HEPM cells, and DPSCs. Loss of METTL3 led to reduced mRNA m6A methylation and PSEN1 expression, impacting craniofacial phenotypes. Co-injection of mettl3 or psen1 mRNA rescued the level of Sox10 fusion protein, promoted voluntary movement, and mitigated abnormal craniofacial phenotypes induced by mettl3 knockdown in zebrafish. Mechanistically, YTHDF1 enhanced the mRNA stability of m6A-modified PSEN1, while decreased METTL3-mediated m6A methylation hindered β-catenin binding to PSEN1, suppressing Wnt/β-catenin signaling. Pharmacological activation of the Wnt/β-catenin pathway partially alleviated the phenotypes of mettl3 morphant and reversed the decreases in cell proliferation and migration induced by METTL3 silencing. This study elucidates the pivotal role of METTL3 in craniofacial development via the METTL3/YTHDF1/PSEN1/β-catenin signaling axis.
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Affiliation(s)
- Lan Ma
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Xi Zhou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Siyue Yao
- The Affiliated Stomatology Hospital of Suzhou Vocational Health College, Suzhou, China
| | - Xinyu Zhang
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Ji Mao
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
| | - Liwen Fan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China.
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.
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Kim H, Hu J, Kang H, Kim W. Phylogenetic and functional analyses of N6-methyladenosine RNA methylation factors in the wheat scab fungus Fusarium graminearum. mSphere 2024; 9:e0055223. [PMID: 38085094 PMCID: PMC10826363 DOI: 10.1128/msphere.00552-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 01/31/2024] Open
Abstract
In eukaryotes, N6-methyladenosine (m6A) RNA modification plays a crucial role in governing the fate of RNA molecules and has been linked to various developmental processes. However, the phyletic distribution and functions of genetic factors responsible for m6A modification remain largely unexplored in fungi. To get insights into the evolution of m6A machineries, we reconstructed global phylogenies of potential m6A writers, readers, and erasers in fungi. Substantial copy number variations were observed, ranging from up to five m6A writers in early-diverging fungi to a single copy in the subphylum Pezizomycotina, which primarily comprises filamentous fungi. To characterize m6A factors in a phytopathogenic fungus Fusarium graminearum, we generated knockout mutants lacking potential m6A factors including the sole m6A writer MTA1. However, the resulting knockouts did not exhibit any noticeable phenotypic changes during vegetative and sexual growth stages. As obtaining a homozygous knockout lacking MTA1 was likely hindered by its essential role, we generated MTA1-overexpressing strains (MTA1-OE). The MTA1-OE5 strain showed delayed conidial germination and reduced hyphal branching, suggesting its involvement during vegetative growth. Consistent with these findings, the expression levels of MTA1 and a potential m6A reader YTH1 were dramatically induced in germinating conidia, followed by the expression of potential m6A erasers at later vegetative stages. Several genes including transcription factors, transporters, and various enzymes were found to be significantly upregulated and downregulated in the MTA1-OE5 strain. Overall, our study highlights the functional importance of the m6A methylation during conidial germination in F. graminearum and provides a foundation for future investigations into m6A modification sites in filamentous fungi.IMPORTANCEN6-methyladenosine (m6A) RNA methylation is a reversible posttranscriptional modification that regulates RNA function and plays a crucial role in diverse developmental processes. This study addresses the knowledge gap regarding phyletic distribution and functions of m6A factors in fungi. The identification of copy number variations among fungal groups enriches our knowledge regarding the evolution of m6A machinery in fungi. Functional characterization of m6A factors in a phytopathogenic filamentous fungus Fusarium graminearum provides insights into the essential role of the m6A writer MTA1 in conidial germination and hyphal branching. The observed effects of overexpressing MTA1 on fungal growth and gene expression patterns of m6A factors throughout the life cycle of F. graminearum further underscore the importance of m6A modification in conidial germination. Overall, this study significantly advances our understanding of m6A modification in fungi, paving the way for future research into its roles in filamentous growth and potential applications in disease control.
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Affiliation(s)
- Hyeonjae Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Jianzhong Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
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Yang Q, Vafaei S, Falahati A, Khosh A, Bariani MV, Omran MM, Bai T, Siblini H, Ali M, He C, Boyer TG, Al-Hendy A. Bromodomain-Containing Protein 9 Regulates Signaling Pathways and Reprograms the Epigenome in Immortalized Human Uterine Fibroid Cells. Int J Mol Sci 2024; 25:905. [PMID: 38255982 PMCID: PMC10815284 DOI: 10.3390/ijms25020905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Bromodomain-containing proteins (BRDs) are involved in many biological processes, most notably epigenetic regulation of transcription, and BRD dysfunction has been linked to many diseases, including tumorigenesis. However, the role of BRDs in the pathogenesis of uterine fibroids (UFs) is entirely unknown. The present study aimed to determine the expression pattern of BRD9 in UFs and matched myometrium and further assess the impact of a BRD9 inhibitor on UF phenotype and epigenetic/epitranscriptomic changes. Our studies demonstrated that the levels of BRD9 were significantly upregulated in UFs compared to matched myometrium, suggesting that the aberrant BRD expression may contribute to the pathogenesis of UFs. We then evaluated the potential roles of BRD9 using its specific inhibitor, I-BRD9. Targeted inhibition of BRD9 suppressed UF tumorigenesis with increased apoptosis and cell cycle arrest, decreased cell proliferation, and extracellular matrix deposition in UF cells. The latter is the key hallmark of UFs. Unbiased transcriptomic profiling coupled with downstream bioinformatics analysis further and extensively demonstrated that targeted inhibition of BRD9 impacted the cell cycle- and ECM-related biological pathways and reprogrammed the UF cell epigenome and epitranscriptome in UFs. Taken together, our studies support the critical role of BRD9 in UF cells and the strong interconnection between BRD9 and other pathways controlling the UF progression. Targeted inhibition of BRDs might provide a non-hormonal treatment option for this most common benign tumor in women of reproductive age.
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Affiliation(s)
- Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
| | - Somayeh Vafaei
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
| | - Ali Falahati
- DNA GTx LAB, Dubai Healthcare City, Dubai 505262, United Arab Emirates;
| | - Azad Khosh
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (A.K.); (T.G.B.)
| | - Maria Victoria Bariani
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
| | - Mervat M. Omran
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Tao Bai
- Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Hiba Siblini
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
| | - Mohamed Ali
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA;
| | - Thomas G. Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (A.K.); (T.G.B.)
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA; (S.V.); (M.V.B.); (M.M.O.); (H.S.); (M.A.); (A.A.-H.)
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Krusnauskas R, Stakaitis R, Steponaitis G, Almstrup K, Vaitkiene P. Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq. Epigenetics 2023; 18:2163365. [PMID: 36597408 PMCID: PMC9980576 DOI: 10.1080/15592294.2022.2163365] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.
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Affiliation(s)
- Raulas Krusnauskas
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Rytis Stakaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Giedrius Steponaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (Edmarc), Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Paulina Vaitkiene
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
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Luo W, Tang Y, Li S, Zhang L, Liu Y, Zhang R, Diao X, Yu J. The m 6 A reader SiYTH1 enhances drought tolerance by affecting the messenger RNA stability of genes related to stomatal closure and reactive oxygen species scavenging in Setaria italica. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2569-2586. [PMID: 37861067 DOI: 10.1111/jipb.13575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023]
Abstract
Foxtail millet (Setaria italica), a vital drought-resistant crop, plays a significant role in ensuring food and nutritional security. However, its drought resistance mechanism is not fully understood. N6 -methyladenosine (m6 A) modification of RNA, a prevalent epi-transcriptomic modification in eukaryotes, provides a binding site for m6 A readers and affects plant growth and stress responses by regulating RNA metabolism. In this study, we unveiled that the YT521-B homology (YTH) family gene SiYTH1 positively regulated the drought tolerance of foxtail millet. Notably, the siyth1 mutant exhibited reduced stomatal closure and augmented accumulation of excessive H2 O2 under drought stress. Further investigations demonstrated that SiYTH1 positively regulated the transcripts harboring m6 A modification related to stomatal closure and reactive oxygen species (ROS) scavenging under drought stress. SiYTH1 was uniformly distributed in the cytoplasm of SiYTH1-GFP transgenic foxtail millet. It formed dynamic liquid-like SiYTH1 cytosol condensates in response to drought stress. Moreover, the cytoplasmic protein SiYTH1 was identified as a distinct m6 A reader, facilitating the stabilization of its directly bound SiARDP and ROS scavenging-related transcripts under drought stress. Furthermore, natural variation analysis revealed SiYTH1AGTG as the dominant allele responsible for drought tolerance in foxtail millet. Collectively, this study provides novel insights into the intricate mechanism of m6 A reader-mediated drought tolerance and presents a valuable genetic resource for improving drought tolerance in foxtail millet breeding.
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Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuxiang Tang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shenglan Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Linlin Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuwei Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Renliang Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingjuan Yu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Xiong QP, Li J, Li H, Huang ZX, Dong H, Wang ED, Liu RJ. Human TRMT1 catalyzes m 2G or m 22G formation on tRNAs in a substrate-dependent manner. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2295-2309. [PMID: 37204604 DOI: 10.1007/s11427-022-2295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/30/2023] [Indexed: 05/20/2023]
Abstract
TRMT1 is an N2-methylguanosine (m2G) and N2,N2-methylguanosine (m22G) methyltransferase that targets G26 of both cytoplasmic and mitochondrial tRNAs. In higher eukaryotes, most cytoplasmic tRNAs with G26 carry m22G26, although the majority of mitochondrial G26-containing tRNAs carry m2G26 or G26, suggesting differences in the mechanisms by which TRMT1 catalyzes modification of these tRNAs. Loss-of-function mutations of human TRMT1 result in neurological disorders and completely abrogate tRNA:m22G26 formation. However, the mechanism underlying the independent catalytic activity of human TRMT1 and identity of its specific substrate remain elusive, hindering a comprehensive understanding of the pathogenesis of neurological disorders caused by TRMT1 mutations. Here, we showed that human TRMT1 independently catalyzes formation of the tRNA:m2G26 or m22G26 modification in a substrate-dependent manner, which explains the distinct distribution of m2G26 and m22G26 on cytoplasmic and mitochondrial tRNAs. For human TRMT1-mediated tRNA:m22G26 formation, the semi-conserved C11:G24 serves as the determinant, and the U10:A25 or G10:C25 base pair is also required, while the size of the variable loop has no effect. We defined the requirements of this recognition mechanism as the "m22G26 criteria". We found that the m22G26 modification occurred in almost all the higher eukaryotic tRNAs conforming to these criteria, suggesting the "m22G26 criteria" are applicable to other higher eukaryotic tRNAs.
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Affiliation(s)
- Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhi-Xuan Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Han Dong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Xie F, Zheng Y, Fu W, Chi B, Wang X, Zhang J, Gu J, Yin J, Zhou Q, Guo S, Cai L, Yang J, Liu S, Wang H. The m6A methyltransferase METTL16 inhibits the proliferation of pancreatic adenocarcinoma cancer cells via the p21 signaling pathway. Front Oncol 2023; 13:1138238. [PMID: 37182151 PMCID: PMC10166879 DOI: 10.3389/fonc.2023.1138238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023] Open
Abstract
Background Many studies have reported that N6-methyladenosine (m6A) modification plays a critical role in the epigenetic regulation of organisms and especially in the pathogenesis of malignant diseases. However, m6A research has mainly focused on methyltransferase activity mediated by METTL3, and few studies have focused on METTL16. The aim of this study was to investigate the mechanism of METTL16, which mediates m6A modification, and its role in pancreatic adenocarcinoma (PDAC) cell proliferation. Methods Clinicopathologic and survival data were retrospectively collected from 175 PDAC patients from multiple clinical centers to detect the expression of METTL16. CCK-8, cell cycle, EdU and xenograft mouse model experiments were used to evaluate the proliferation effect of METTL16. Potential downstream pathways and mechanisms were explored via RNA sequencing, m6A sequencing, and bioinformatic analyses. Regulatory mechanisms were studied through methyltransferase inhibition, RIP, MeRIP‒qPCR assays. Results We found that METTL16 expression was markedly downregulated in PDAC, and multivariate Cox regression analyses revealed that METTL16 was a protective factor for PDAC patients. We also demonstrated that METTL16 overexpression inhibited PDAC cell proliferation. Furthermore, we identified a METTL16-p21 signaling axis, with downregulation of METTL16 resulting in inhibition of CDKN1A (p21). Additionally, METTL16 silencing and overexpression experiments highlighted m6A modification alterations in PDAC. Conclusions METTL16 plays a tumor-suppressive role and suppresses PDAC cell proliferation through the p21 pathway by mediating m6A modification. METTL16 may be a novel marker of PDAC carcinogenesis and target for the treatment of PDAC.
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Affiliation(s)
- Fuming Xie
- University of Chinese Academy of Sciences (UCAS) Chongqing School, Chongqing Medical University, Chongqing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences (CAS), Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing, China
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
| | - Yao Zheng
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing General Hospital, Chongqing, China
| | - Wen Fu
- University of Chinese Academy of Sciences (UCAS) Chongqing School, Chongqing Medical University, Chongqing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences (CAS), Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing, China
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
| | - Bojing Chi
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Savaid Medical School, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xianxing Wang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing General Hospital, Chongqing, China
| | - Junfeng Zhang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
| | - Jianyou Gu
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
| | - Jingyang Yin
- University of Chinese Academy of Sciences (UCAS) Chongqing School, Chongqing Medical University, Chongqing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences (CAS), Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing, China
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
| | - Qiang Zhou
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing General Hospital, Chongqing, China
| | - Shixiang Guo
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing General Hospital, Chongqing, China
| | - Lei Cai
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
| | - Jiali Yang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing General Hospital, Chongqing, China
| | - Songsong Liu
- Department of Hepatobiliary Surgery, Hainan Hospital of People’s Liberation Army of China (PLA) General Hospital, Sanya, China
| | - Huaizhi Wang
- University of Chinese Academy of Sciences (UCAS) Chongqing School, Chongqing Medical University, Chongqing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences (CAS), Chongqing, China
- Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing, China
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing General Hospital, Chongqing, China
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9
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Cheng B, Xie M, Zhou Y, Li T, Liu W, Yu W, Jia M, Yu S, Chen L, Dai R, Wang R. Vascular mimicry induced by m 6A mediated IGFL2-AS1/AR axis contributes to pazopanib resistance in clear cell renal cell carcinoma. Cell Death Discov 2023; 9:121. [PMID: 37037853 PMCID: PMC10086028 DOI: 10.1038/s41420-023-01423-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/12/2023] Open
Abstract
Metastatic clear cell renal cell carcinoma (ccRCC) is a lethal sub-type of kidney cancer. Vascular mimicry (VM) has been postulated as an alternative route to supply tumors with nutrients, playing key role in tumor development. Whether VM development is linked to pazopanib efficacy, however, remains unclear. Here, our in vitro and in vivo models identified that VM development was profoundly increased in pazopanib resistant ccRCC as compared to the sensitive controls, which was due to the activation of IGFL2-AS1/AR/TWIST1 signaling. IGFL2-AS1, a m6A modified long coding RNA, was demethylated by METTL3/METTL14 complex and stabilized owing to its failing recognition by YTHDF2 upon chronic pazopanib treatment. Further mechanistic dissection illustrated that IGFL2-AS1 physically interacted with the 5'-UTR AR mRNA and neutralized the negative regulation of 5'-uORF (upstream open reading frame) on AR translation. Indeed, IGFL2-AS1 short of AR binding region failed to promote AR expression, VM formation and pazopanib resistance. In vivo xenografted mouse model also elucidated that inhibition of AR activity with enzalutamide or silence of IGFL2-AS1 with siRNAs all led to retarded growth of pazopanib resistant ccRCC tumors. Together, these results suggest that IGFL2-AS1 may represent a key player to mediate pazopanib-induced VM formation of ccRCC cells via regulating AR expression and targeting this newly identified IGFL2-AS1/AR signaling may help us to better suppress ccRCC VM formation and to increase the therapeutic efficacy of pazopanib.
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Affiliation(s)
- Bo Cheng
- Department of Urology, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Mingyue Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Yong Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Tian Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Wanting Liu
- Department of Urology, the Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Wenjing Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Man Jia
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Shuang Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Lixuan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China
| | - Rongyang Dai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
| | - Ronghao Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
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10
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Tang Z, Sun C, Yan Y, Niu Z, Li Y, Xu X, Zhang J, Wu Y, Li Y, Wang L, Hu C, Li Z, Jiang J, Ying H. Aberrant elevation of FTO levels promotes liver steatosis by decreasing the m6A methylation and increasing the stability of SREBF1 and ChREBP mRNAs. J Mol Cell Biol 2023; 14:6817255. [PMID: 36352530 PMCID: PMC9951264 DOI: 10.1093/jmcb/mjac061] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/23/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
Previous studies have indicated an association of fat mass and obesity-associated (FTO) with nonalcoholic fatty liver disease (NAFLD), the most common chronic liver disease worldwide. This study aimed to decipher the complex role of FTO in hepatic lipid metabolism. We found that a decrease in N6-methyladenosine (m6A) RNA methylation in the liver of mice fed with a high-fat diet (HFD) was accompanied by an increase in FTO expression. Overexpression of FTO in the liver promoted triglyceride accumulation by upregulating the expression of lipogenic genes. Mechanistical studies revealed that FTO could stabilize the mRNAs of sterol regulatory element binding transcription factor 1 (SREBF1) and carbohydrate responsive element binding protein (ChREBP), two master lipogenic transcription factors, by demethylating m6A sites. Knockdown of either SREBF1 or ChREBP attenuated the lipogenic effect of FTO, suggesting that they are bona fide effectors for FTO in regulating lipogenesis. Insulin could stimulate FTO transcription through a mechanism involving the action of intranuclear insulin receptor beta, while knockdown of FTO abrogated the lipogenic effect of insulin. Inhibition of FTO by entacapone decreased the expression of SREBF1, ChREBP, and downstream lipogenic genes, ameliorating liver steatosis in HFD-fed mice. Thus, our study established a critical role of FTO in both the insulin-regulated hepatic lipogenesis and the pathogenesis of NAFLD and provided a potential strategy for treating NAFLD.
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Affiliation(s)
- Zhili Tang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China.,Innovation Center for Intervention of Chronic Disease and Promotion of Health, Shanghai 200031, China
| | - Chao Sun
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China
| | - Ying Yan
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China
| | - Zhoumin Niu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China
| | - Yuying Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China
| | - Xi Xu
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200031, China
| | - Jing Zhang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200031, China
| | - Yuting Wu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Zhuoyang Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200031, China
| | - Hao Ying
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200031, China.,Innovation Center for Intervention of Chronic Disease and Promotion of Health, Shanghai 200031, China.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
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11
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Ren W, Yuan Y, Li Y, Mutti L, Peng J, Jiang X. The function and clinical implication of YTHDF1 in the human system development and cancer. Biomark Res 2023; 11:5. [PMID: 36650570 PMCID: PMC9847098 DOI: 10.1186/s40364-023-00452-1] [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: 09/28/2022] [Accepted: 11/26/2022] [Indexed: 01/19/2023] Open
Abstract
YTHDF1 is a well-characterized m6A reader protein that is essential for protein translation, stem cell self-renewal, and embryonic development. YTHDF1 regulates target gene expression by diverse molecular mechanisms, such as promoting protein translation or modulating the stability of mRNA. The cellular levels of YTHDF1 are precisely regulated by a complicated transcriptional, post-transcriptional, and post-translational network. Very solid evidence supports the pivotal role of YTHDF1 in embryonic development and human cancer progression. In this review, we discuss how YTHDF1 influences both the physiological and pathological biology of the central nervous, reproductive and immune systems. Therefore we focus on some relevant aspects of the regulatory role played by YTHDF1 as gene expression, complex cell networking: stem cell self-renewal, embryonic development, and human cancers progression. We propose that YTHDF1 is a promising future cancer biomarker for detection, progression, and prognosis. Targeting YTHDF1 holds therapeutic potential, as the overexpression of YTHDF1 is associated with tumor resistance to chemotherapy and immunotherapy.
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Affiliation(s)
- Wenjun Ren
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Yixiao Yuan
- grid.452206.70000 0004 1758 417XKey Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongwu Li
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Luciano Mutti
- grid.264727.20000 0001 2248 3398Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA ,grid.158820.60000 0004 1757 2611Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2 67100 L’Aquila, Italy
| | - Jun Peng
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Xiulin Jiang
- grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
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12
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Ferraz R, Coimbra S, Correia S, Canhoto J. RNA methyltransferases in plants: Breakthroughs in function and evolution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:449-460. [PMID: 36502609 DOI: 10.1016/j.plaphy.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Each day it is becoming increasingly difficult not to notice the completely new, fast growing, extremely intricate and challenging world of epitranscriptomics as the understanding of RNA methylation is expanding at a hasty rate. Writers (methyltransferases), erasers (demethylases) and readers (RNA-binding proteins) are responsible for adding, removing and recognising methyl groups on RNA, respectively. Several methyltransferases identified in plants are now being investigated and recent studies have shown a connection between RNA-methyltransferases (RNA-MTases) and stress and development processes. However, compared to their animal and bacteria counterparts, the understanding of RNA methyltransferases is still incipient, particularly those located in organelles. Comparative and systematic analyses allowed the tracing of the evolution of these enzymes suggesting the existence of several methyltransferases yet to be characterised. This review outlines the functions of plant nuclear and organellar RNA-MTases in plant development and stress responses and the comparative and evolutionary discoveries made on RNA-MTases across kingdoms.
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Affiliation(s)
- Ricardo Ferraz
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sílvia Coimbra
- University of Porto, Faculty of Sciences, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
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13
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Ouyang H, Zhang J, Chi D, Zhang K, Huang Y, Huang J, Huang W, Bai X. The YTHDF1-TRAF6 pathway regulates the neuroinflammatory response and contributes to morphine tolerance and hyperalgesia in the periaqueductal gray. J Neuroinflammation 2022; 19:310. [PMID: 36550542 PMCID: PMC9784087 DOI: 10.1186/s12974-022-02672-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Long-term use of opioids such as morphine has negative side effects, such as morphine analgesic tolerance and morphine-induced hyperalgesia (MIH). These side effects limit the clinical use and analgesic efficacy of morphine. Elucidation of the mechanisms and identification of feasible and effective methods or treatment targets to solve this clinical phenomenon are important. Here, we discovered that YTHDF1 and TNF receptor-associated factor 6 (TRAF6) are crucial for morphine analgesic tolerance and MIH. The m6A reader YTHDF1 positively regulated the translation of TRAF6 mRNA, and chronic morphine treatments enhanced the m6A modification of TRAF6 mRNA. TRAF6 protein expression was drastically reduced by YTHDF1 knockdown, although TRAF6 mRNA levels were unaffected. By reducing inflammatory markers such as IL-1β, IL-6, TNF-α and NF-κB, targeted reduction of YTHDF1 or suppression of TRAF6 activity in ventrolateral periaqueductal gray (vlPAG) slows the development of morphine analgesic tolerance and MIH. Our findings provide new insights into the mechanism of morphine analgesic tolerance and MIH indicating that YTHDF1 regulates inflammatory factors such as IL-1β, IL-6, TNF-α and NF-κB by enhancing TRAF6 protein expression.
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Affiliation(s)
- Handong Ouyang
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Jianxing Zhang
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Dongmei Chi
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Kun Zhang
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Yongtian Huang
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Jingxiu Huang
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Wan Huang
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China
| | - Xiaohui Bai
- grid.488530.20000 0004 1803 6191Department of Anesthesiology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Rd East, Guangzhou, China ,grid.412536.70000 0004 1791 7851Department of Anesthesiology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yangjiang Road West, Guangzhou, China
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14
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Jiang FQ, Liu K, Chen JX, Cao Y, Chen WY, Zhao WL, Song GH, Liang CQ, Zhou YM, Huang HL, Huang RJ, Zhao H, Park KS, Ju Z, Cai D, Qi XF. Mettl3-mediated m6A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration. eLife 2022; 11:77014. [PMCID: PMC9674341 DOI: 10.7554/elife.77014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Cardiovascular disease is the leading cause of death worldwide due to the inability of adult heart to regenerate after injury. N6-methyladenosine (m6A) methylation catalyzed by the enzyme methyltransferase-like 3 (Mettl3) plays an important role in various physiological and pathological bioprocesses. However, the role of m6A in heart regeneration remains largely unclear. To study m6A function in heart regeneration, we modulated Mettl3 expression in vitro and in vivo. Knockdown of Mettl3 significantly increased the proliferation of cardiomyocytes and accelerated heart regeneration following heart injury in neonatal and adult mice. However, Mettl3 overexpression decreased cardiomyocyte proliferation and suppressed heart regeneration in postnatal mice. Conjoint analysis of methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-seq identified Fgf16 as a downstream target of Mettl3-mediated m6A modification during postnatal heart regeneration. RIP-qPCR and luciferase reporter assays revealed that Mettl3 negatively regulates Fgf16 mRNA expression in an m6A-Ythdf2-dependent manner. The silencing of Fgf16 suppressed the proliferation of cardiomyocytes. However, the overexpression of ΔFgf16, in which the m6A consensus sequence was mutated, significantly increased cardiomyocyte proliferation and accelerated heart regeneration in postnatal mice compared with wild-type Fgf16. Our data demonstrate that Mettl3 post-transcriptionally reduces Fgf16 mRNA levels through an m6A-Ythdf2-dependen pathway, thereby controlling cardiomyocyte proliferation and heart regeneration.
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Affiliation(s)
- Fu-Qing Jiang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Kun Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Jia-Xuan Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Yan Cao
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Wu-Yun Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Wan-Ling Zhao
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Guo-Hua Song
- College of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Science
| | - Chi-Qian Liang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Yi-Min Zhou
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Huan-Lei Huang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences
| | - Rui-Jin Huang
- Department of Neuroanatomy, Institute of Anatomy, University of Bonn
| | - Hui Zhao
- Stem Cell and Regeneration TRP, School of Biomedical Sciences, Chinese University of Hong Kong
| | - Kyu-Sang Park
- Department of Physiology, Wonju College of Medicine, Yonsei University
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine
| | - Dongqing Cai
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
| | - Xu-Feng Qi
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University
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15
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Liu H, Zheng YL, Wang XQ. The emerging roles of N 6-methyladenosine in osteoarthritis. Front Mol Neurosci 2022; 15:1040699. [PMID: 36466802 PMCID: PMC9710225 DOI: 10.3389/fnmol.2022.1040699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 08/30/2023] Open
Abstract
Finding new biomarkers and molecular targets to guide OA treatment remains a significant challenge. One of the most frequent forms of RNA methylation, N6-methyladenosine (m6A), can affect gene expression and RNA transcription, processing, translation, and metabolism. Osteoarthritis (OA) can cause disability and pain degenerative disease, reduce the quality of life of the elderly, and increase the social and economic burden. Changes in m6A levels are crucial in OA progress. In this review, the discussion will concentrate on the role that m6A plays in OA occurrence and progression. The m6A involved in the OA process mainly includes METTL3 and FTO. Current studies on m6A and OA primarily focus on four signaling pathways, namely, NF-κB, LNCRNAs, ATG7, and Bcl2. m6A participates in these signaling pathways and affects cellular inflammation, apoptosis, senescence, and autophagy, thus controlling the OA process. The modification of m6A affects so many signaling pathways. For the treatment of OA, it may represent a viable new therapeutic target.
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Affiliation(s)
- Hui Liu
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
| | - Yi-Li Zheng
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
- Department of Rehabilitation Medicine, Shanghai Shangti Orthopaedic Hospital, Shanghai, China
| | - Xue-Qiang Wang
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
- Department of Rehabilitation Medicine, Shanghai Shangti Orthopaedic Hospital, Shanghai, China
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16
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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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17
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Gu L, Zhang S, Li B, Jiang Q, Xu T, Huang Y, Lin D, Xing M, Huang L, Zheng X, Wang F, Chao Z, Sun W. m6A and miRNA jointly regulate the development of breast muscles in duck embryonic stages. Front Vet Sci 2022; 9:933850. [PMID: 36353255 PMCID: PMC9637736 DOI: 10.3389/fvets.2022.933850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/28/2022] [Indexed: 12/01/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant internal mRNA modification and plays a crucial regulatory role in animal growth and development. In recent years, m6A modification has been found to play a key role in skeletal muscles. However, whether m6A modification contributes to embryonic breast muscle development of Pekin ducks has not been explored. To explore the role of m6A in embryonic breast muscle development of ducks, we performed m6A sequencing and miRNA sequencing for the breast muscle of duck embryos on the 19th (E19) and 27th (E27) days. A total of 12,717 m6A peaks were identified at E19, representing a total of 7,438 gene transcripts. A total of 14,703 m6A peaks were identified, which overlapped with the transcripts of 7,753 genes at E27. Comparing E19 and E27, we identified 2,347 differential m6A peaks, which overlapped with 1,605 m6A-modified genes (MMGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that MMGs were enriched in multiple muscle- or fat-related pathways, which was also revealed from our analysis of differentially expressed genes (DEGs). Conjoint analysis of m6A-seq and RNA-seq data showed that pathways related to β-oxidation of fatty acids and skeletal muscle development were significantly enriched, suggesting that m6A modification is involved in the regulation of fat deposition and skeletal muscle development. There were 90 upregulated and 102 downregulated miRNAs identified between the E19 and E27 stages. Through overlapping analysis of genes shared by MMGs and DEGs and the targets of differentially expressed miRNAs (DEMs), we identified six m6A-mRNA-regulated miRNAs. Finally, we found that m6A modification can regulate fat deposition and skeletal muscle development. In conclusion, our results suggest that m6A modification is a key regulator for embryonic breast muscle development and fat deposition of ducks by affecting expressions of mRNAs and miRNAs. This is the first study to comprehensively characterize the m6A patterns in the duck transcriptome. These data provide a solid basis for future work aimed at determining the potential functional roles of m6A modification in adipose deposition and muscle growth.
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Affiliation(s)
- Lihong Gu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Shunjin Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Boling Li
- The Hainan Animal Husbandry Technology Promotion Station, Haikou, China
| | - Qicheng Jiang
- School of Life Science, Hainan University, Haikou, China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Tieshan Xu
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Dajie Lin
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Manping Xing
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Lili Huang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Xinli Zheng
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Feng Wang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Weiping Sun
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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18
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Hao W, Dian M, Zhou Y, Zhong Q, Pang W, Li Z, Zhao Y, Ma J, Lin X, Luo R, Li Y, Jia J, Shen H, Huang S, Dai G, Wang J, Sun Y, Xiao D. Autophagy induction promoted by m 6A reader YTHDF3 through translation upregulation of FOXO3 mRNA. Nat Commun 2022; 13:5845. [PMID: 36195598 PMCID: PMC9532426 DOI: 10.1038/s41467-022-32963-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/24/2022] [Indexed: 12/08/2022] Open
Abstract
Autophagy is crucial for maintaining cellular energy homeostasis and for cells to adapt to nutrient deficiency, and nutrient sensors regulating autophagy have been reported previously. However, the role of eiptranscriptomic modifications such as m6A in the regulation of starvation-induced autophagy is unclear. Here, we show that the m6A reader YTHDF3 is essential for autophagy induction. m6A modification is up-regulated to promote autophagosome formation and lysosomal degradation upon nutrient deficiency. METTL3 depletion leads to a loss of functional m6A modification and inhibits YTHDF3-mediated autophagy flux. YTHDF3 promotes autophagy by recognizing m6A modification sites around the stop codon of FOXO3 mRNA. YTHDF3 also recruits eIF3a and eIF4B to facilitate FOXO3 translation, subsequently initiating autophagy. Overall, our study demonstrates that the epitranscriptome regulator YTHDF3 functions as a nutrient responder, providing a glimpse into the post-transcriptional RNA modifications that regulate metabolic homeostasis.
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Affiliation(s)
- WeiChao Hao
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
| | - MeiJuan Dian
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
- Institute of Comparative Medicine & Laboratory Animal Center, Southern Medical University, 510515, Guangzhou, China
| | - Ying Zhou
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
- Institute of Comparative Medicine & Laboratory Animal Center, Southern Medical University, 510515, Guangzhou, China
| | - QiuLing Zhong
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
| | - WenQian Pang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
| | - ZiJian Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
| | - YaYan Zhao
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, 510080, Guangzhou, China
| | - JiaCheng Ma
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 10084, Beijing, China
| | - XiaoLin Lin
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China
| | - RenRu Luo
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, 518107, Guangdong, China
| | - YongLong Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
- Institute of Comparative Medicine & Laboratory Animal Center, Southern Medical University, 510515, Guangzhou, China
| | - JunShuang Jia
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
| | - HongFen Shen
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
| | - ShiHao Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
- Institute of Comparative Medicine & Laboratory Animal Center, Southern Medical University, 510515, Guangzhou, China
| | - GuanQi Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China
- Institute of Comparative Medicine & Laboratory Animal Center, Southern Medical University, 510515, Guangzhou, China
| | - JiaHong Wang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China.
| | - Yan Sun
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510080, Guangzhou, China.
| | - Dong Xiao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China.
- Institute of Comparative Medicine & Laboratory Animal Center, Southern Medical University, 510515, Guangzhou, China.
- National Demonstration Center for Experimental Education of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, China.
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19
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Zha L, Wang J, Cheng X. The effects of
RNA
methylation on immune cells development and function. FASEB J 2022; 36:e22552. [DOI: 10.1096/fj.202200716r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ling‐Feng Zha
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Jing‐Lin Wang
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Xiang Cheng
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
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20
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Scutenaire J, Plassard D, Matelot M, Villa T, Zumsteg J, Libri D, Séraphin B. The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts. Nucleic Acids Res 2022; 51:517-535. [PMID: 35934316 PMCID: PMC9881176 DOI: 10.1093/nar/gkac640] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
N6-Methyladenosine (m6A), one of the most abundant internal modification of eukaryotic mRNAs, participates in the post-transcriptional control of gene expression through recruitment of specific m6A readers. In Saccharomyces cerevisiae, the m6A methyltransferase Ime4 is expressed only during meiosis and its deletion impairs this process. To elucidate how m6A control gene expression, we investigated the function of the budding yeast m6A reader Pho92. We show that Pho92 is an early meiotic factor that promotes timely meiotic progression. High-throughput RNA sequencing and mapping of Pho92-binding sites following UV-crosslinking reveal that Pho92 is recruited to specific mRNAs in an m6A-dependent manner during the meiotic prophase, preceding their down-regulation. Strikingly, point mutations altering m6A sites in mRNAs targeted by Pho92 are sufficient to delay their down-regulation and, in one case, to slow down meiotic progression. Altogether, our results indicate that Pho92 facilitate the meiotic progression by accelerating the down-regulation of timely-regulated mRNAs during meiotic recombination.
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Affiliation(s)
- Jérémy Scutenaire
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France,Centre National de Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch, France,Institut National de Santé et de Recherche Médicale (INSERM) U1258, 67400 Illkirch, France,Université de Strasbourg, 67400 Illkirch, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France,Centre National de Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch, France,Institut National de Santé et de Recherche Médicale (INSERM) U1258, 67400 Illkirch, France,Université de Strasbourg, 67400 Illkirch, France
| | - Mélody Matelot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France,Centre National de Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch, France,Institut National de Santé et de Recherche Médicale (INSERM) U1258, 67400 Illkirch, France,Université de Strasbourg, 67400 Illkirch, France
| | - Tommaso Villa
- Université de Paris Cité, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Domenico Libri
- Université de Paris Cité, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Bertrand Séraphin
- To whom correspondence should be addressed. Tel: +33 3 88 65 33 36; Fax: +33 3 88 65 32 01;
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21
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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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22
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Alagia A, Gullerova M. The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine. Front Cell Dev Biol 2022; 10:915685. [PMID: 35721489 PMCID: PMC9204050 DOI: 10.3389/fcell.2022.915685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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23
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Shafik AM, Zhou H, Lim J, Dickinson B, Jin P. Dysregulated mitochondrial and cytosolic tRNA m1A methylation in Alzheimer's disease. Hum Mol Genet 2022; 31:1673-1680. [PMID: 34897434 PMCID: PMC9122638 DOI: 10.1093/hmg/ddab357] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/22/2021] [Accepted: 12/08/2021] [Indexed: 12/15/2022] Open
Abstract
RNA modifications affect many aspects of RNA metabolism and are involved in the regulation of many different biological processes. Mono-methylation of adenosine in the N1 position, N1-methyladensoine (m1A), is a reversible modification that is known to target rRNAs and tRNAs. m1A has been shown to increase tRNA structural stability and induce correct tRNA folding. Recent studies have begun to associate the dysregulation of epitranscriptomic control with age-related disorders such as Alzheimer's disease. Here, we applied the newly developed m1A-quant-seq approach to map the brain abundant m1A RNA modification in the cortex of an Alzheimer's disease mouse model, 5XFAD. We observed hypomethylation in both mitochondrial and cytosolic tRNAs in 5XFAD mice compared with wild type. Furthermore, the main enzymes responsible for the addition of m1A in mitochondrial (TRMT10C, HSD17B10) and cytosolic tRNAs (TRMT61A) displayed decreased expression in 5XFAD compared with wild-type mice. Knockdown of these enzymes results in a more severe phenotype in a Drosophila tau model, and differential m1A methylation is correlated with differences in mature mitochondrial tRNA expression. Collectively, this work suggests that hypo m1A modification in tRNAs may play a role in Alzheimer's disease pathogenesis.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 3032, USA
| | - Huiqing Zhou
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Junghwa Lim
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 3032, USA
| | - Bryan Dickinson
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 3032, USA
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24
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Han Y, Xia L, Wang X, Xiong H, Zeng L, Wang Z, Zhang T, Xia K, Hu X, Su T. Study on the expression and function of chordin like 1 in oral squamous cell carcinoma. Oral Dis 2022. [PMID: 35510812 DOI: 10.1111/odi.14240] [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: 01/22/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the role and related mechanism of chordin like 1 (CHRDL1) in oral squamous cell carcinoma (OSCC). METHODS The expressions of CHRDL1 were analyzed in both mRNA and protein levels by bioinformatics analysis, immunohistochemistry, and fluorescence in situ hybridization in OSCC. Survival analysis was used to determine the relationship between CHRDL1 and prognosis. In addition, enrichment analysis was used to suggest signal pathways involved in CHRDL1. Besides, the relationships between CHRDL1 and miRNAs, hypoxia, and immune infiltration were explored. RESULTS The mRNA level of CHRDL1 in OSCC was significantly lower than that in normal tissues, while the protein level was significantly higher than that in normal tissues. The high mRNA levels of CHRDL1 suggested a poor prognosis in patients with OSCC. The enrichment results showed that CHRDL1 might be involved in the Calcium signaling pathway, dilated cardiomyopathy, and focal adhesion. 7 immune cells were positively correlated with CHRDL1, while Tgd was negatively correlated with CHRDL1. In addition, we also found that hsa-miR-455-3p directly targeted CHRDL1 and reduced the mRNA levels of CHRDL1. CONCLUSION CHRDL1 plays a vital role in promoting cancer in OSCC and is downregulated at the mRNA levels by hsa-miR-455-3p.
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Affiliation(s)
- Ying Han
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Haofeng Xiong
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, China
| | - Liujun Zeng
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, China
| | - Zijia Wang
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, China
| | - Tianyi Zhang
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Xin Hu
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, China
| | - Tong Su
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya hospital of Central South University, Changsha, Hunan, 410008, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, Hunan, 410008, China
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25
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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26
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Yang Q, Al-Hendy A. The Regulatory Functions and the Mechanisms of Long Non-Coding RNAs in Cervical Cancer. Cells 2022; 11:cells11071149. [PMID: 35406713 PMCID: PMC8998012 DOI: 10.3390/cells11071149] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/11/2022] Open
Abstract
Cervical cancer is one of the leading causes of death in gynecology cancer worldwide. High-risk human papillomaviruses (HPVs) are the major etiological agents for cervical cancer. Still, other factors also contribute to cervical cancer development because these cancers commonly arise decades after initial exposure to HPV. So far, the molecular mechanisms underlying the pathogenesis of cervical cancer are still quite limited, and a knowledge gap needs to be filled to help develop novel strategies that will ultimately facilitate the development of therapies and improve cervical cancer patient outcomes. Long non-coding RNAs (lncRNAs) have been increasingly shown to be involved in gene regulation, and the relevant role of lncRNAs in cervical cancer has recently been investigated. In this review, we summarize the recent progress in ascertaining the biological functions of lncRNAs in cervical cancer from the perspective of cervical cancer proliferation, invasion, and metastasis. In addition, we provide the current state of knowledge by discussing the molecular mechanisms underlying the regulation and emerging role of lncRNAs in the pathogenesis of cervical cancer. Comprehensive and deeper insights into lncRNA-mediated alterations and interactions in cellular events will help develop novel strategies to treat patients with cervical cancer.
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27
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Chemical modifications to mRNA nucleobases impact translation elongation and termination. Biophys Chem 2022; 285:106780. [DOI: 10.1016/j.bpc.2022.106780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/13/2022] [Indexed: 12/15/2022]
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28
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Xu Y, He X, Wang S, Sun B, Jia R, Chai P, Li F, Yang Y, Ge S, Jia R, Yang YG, Fan X. The m 6A reading protein YTHDF3 potentiates tumorigenicity of cancer stem-like cells in ocular melanoma through facilitating CTNNB1 translation. Oncogene 2022; 41:1281-1297. [PMID: 35110680 DOI: 10.1038/s41388-021-02146-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/06/2021] [Accepted: 12/02/2021] [Indexed: 01/03/2023]
Abstract
N6-methyladenosine (m6A) is the most universal internal RNA modification on messenger RNAs and regulates the fate and functions of m6A-modified transcripts through m6A-specific binding proteins. Nevertheless, the functional role and potential mechanism of the m6A reading proteins in ocular melanoma tumorigenicity, especially cancer stem-like cell (CSC) properties, remain to be elucidated. Herein, we demonstrated that the m6A reading protein YTHDF3 promotes the translation of the target transcript CTNNB1, contributing to ocular melanoma propagation and migration through m6A methylation. YTHDF3 is highly expressed in ocular melanoma stem-like cells and abundantly enriched in ocular melanoma tissues, which is related to poor clinical prognosis. Moreover, YTHDF3 is required for the maintenance of CSC properties and tumor initiation capacity in ocular melanoma both in vitro and in vivo. Ocular melanoma cells with targeted YTHDF3 knockdown exhibited inhibitory tumor proliferation and migration abilities. Transcriptome-wide mapping of m6A peaks and YTHDF3 binding peaks on mRNAs revealed a key target gene candidate, CTNNB1. Mechanistically, YTHDF3 enhances CTNNB1 translation through recognizing and binding the m6A peaks on CTNNB1 mRNA.
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Affiliation(s)
- Yangfan Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Xiaoyu He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Shanzheng Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
- China National Center for Bioinformation, Beijing, P.R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Baofa Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
- China National Center for Bioinformation, Beijing, P.R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, P.R. China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Fang Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
- China National Center for Bioinformation, Beijing, P.R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, P.R. China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, P.R. China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China.
- China National Center for Bioinformation, Beijing, P.R. China.
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, P.R. China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, P.R. China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, P.R. China.
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29
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Huang JB, Hu BB, He R, He L, Zou C, Man CF, Fan Y. Analysis of N6-Methyladenosine Methylome in Adenocarcinoma of Esophagogastric Junction. Front Genet 2022; 12:787800. [PMID: 35140740 PMCID: PMC8820482 DOI: 10.3389/fgene.2021.787800] [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: 11/08/2021] [Accepted: 12/30/2021] [Indexed: 11/21/2022] Open
Abstract
Background: From previous studies, we found that there are more than 100 types of RNA modifications in RNA molecules. m6A methylation is the most common. The incidence rate of adenocarcinoma of the esophagogastric junction (AEG) at home and abroad has increased faster than that of stomach cancer at other sites in recent years. Here, we systematically analyze the modification pattern of m6A mRNA in adenocarcinoma at the esophagogastric junction. Methods: m6A sequencing, RNA sequencing, and bioinformatics analysis were used to describe the m6A modification pattern in adenocarcinoma and normal tissues at the esophagogastric junction. Results: In AEG samples, a total of 4,775 new m6A peaks appeared, and 3,054 peaks disappeared. The unique m6A-related genes in AEG are related to cancer-related pathways. There are hypermethylated or hypomethylated m6A peaks in AEG in differentially expressed mRNA transcripts. Conclusion: This study preliminarily constructed the first m6A full transcriptome map of human AEG. This has a guiding role in revealing the mechanism of m6A-mediated gene expression regulation.
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30
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Rowe L, Rockwell AL. Ubiquitous Knockdown of Mettl3 using TRiP.GL01126 Results in Spermatid Mislocalization During Drosophila Spermatogenesis. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000511. [PMID: 35071998 PMCID: PMC8767421 DOI: 10.17912/micropub.biology.000511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/02/2022] [Accepted: 01/07/2022] [Indexed: 11/06/2022]
Abstract
METTL3, the enzyme that catalyzes the m6A RNA modification in Drosophila is highly conserved and essential in various eukaryotic organisms. Mettl3 and its homologs have been linked to biological processes such as gametogenesis. We focused on characterizing the role of METTL3 in Drosophila spermatogenesis. We used the Gal4-UAS system to ubiquitously knockdown Mettl3 in both somatic cyst cells and germline cells. Using immunostaining and confocal microscopy, we found spermatid bundles mislocalize in testes that contain the morphologically abnormal swollen apical tip. Our result suggests Mettl3 knockdown using TRiP.GL01126 results in spermatogenesis aberrations.
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31
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Peters A, Herrmann E, Cornelissen NV, Klöcker N, Kümmel D, Rentmeister A. Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Chembiochem 2022; 23:e202100437. [PMID: 34606675 PMCID: PMC9298006 DOI: 10.1002/cbic.202100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo-cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non-damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non-natural groups, including first evidence for accepting photo-cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC-MjMAT) is 308-fold more efficient at converting ortho-nitrobenzyl-(ONB)-homocysteine than the wildtype enzyme. PC-MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC-MjMAT in complex with AdoONB and a red-shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC-MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC-MjMAT exhibits remarkable activity on methionine analogues with red-shifted ONB-derivatives enabling photo-deprotection of modified DNA by visible light.
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Affiliation(s)
- Aileen Peters
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 3648149MünsterGermany
| | - Eric Herrmann
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 3648149MünsterGermany
| | - Nicolas V. Cornelissen
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 3648149MünsterGermany
| | - Nils Klöcker
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 3648149MünsterGermany
| | - Daniel Kümmel
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 3648149MünsterGermany
| | - Andrea Rentmeister
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 3648149MünsterGermany
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32
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Hendra C, Pratanwanich PN, Wan YK, Goh WSS, Thiery A, Göke J. Detection of m6A from direct RNA sequencing using a multiple instance learning framework. Nat Methods 2022; 19:1590-1598. [PMID: 36357692 PMCID: PMC9718678 DOI: 10.1038/s41592-022-01666-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/27/2022] [Indexed: 11/12/2022]
Abstract
RNA modifications such as m6A methylation form an additional layer of complexity in the transcriptome. Nanopore direct RNA sequencing can capture this information in the raw current signal for each RNA molecule, enabling the detection of RNA modifications using supervised machine learning. However, experimental approaches provide only site-level training data, whereas the modification status for each single RNA molecule is missing. Here we present m6Anet, a neural-network-based method that leverages the multiple instance learning framework to specifically handle missing read-level modification labels in site-level training data. m6Anet outperforms existing computational methods, shows similar accuracy as experimental approaches, and generalizes with high accuracy to different cell lines and species without retraining model parameters. In addition, we demonstrate that m6Anet captures the underlying read-level stoichiometry, which can be used to approximate differences in modification rates. Overall, m6Anet offers a tool to capture the transcriptome-wide identification and quantification of m6A from a single run of direct RNA sequencing.
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Affiliation(s)
- Christopher Hendra
- grid.4280.e0000 0001 2180 6431Institute of Data Science, National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, A*STAR, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Ploy N. Pratanwanich
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, A*STAR, Singapore, Singapore ,grid.7922.e0000 0001 0244 7875Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Chulalongkorn, Thailand ,grid.7922.e0000 0001 0244 7875Chula Intelligent and Complex Systems Research Unit, Chulalongkorn University, Chulalongkorn, Thailand
| | - Yuk Kei Wan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, A*STAR, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431 Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - W. S. Sho Goh
- grid.510951.90000 0004 7775 6738Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Alexandre Thiery
- grid.4280.e0000 0001 2180 6431Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, A*STAR, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Center of Singapore, Singapore, Singapore
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33
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Guo G, Pan K, Fang S, Ye L, Tong X, Wang Z, Xue X, Zhang H. Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:575-593. [PMID: 34631286 PMCID: PMC8479277 DOI: 10.1016/j.omtn.2021.08.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-methylcytosine (m5C) post-transcriptional modifications affect the maturation, stability, and translation of the mRNA molecule. These modifications play an important role in many physiological and pathological processes, including stress response, tumorigenesis, tumor cell migration, embryogenesis, and viral replication. Recently, there has been a better understanding of the biological implications of m5C modification owing to the rapid development and optimization of detection technologies, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-BisSeq. Further, predictive models (such as PEA-m5C, m5C-PseDNC, and DeepMRMP) for the identification of potential m5C modification sites have also emerged. In this review, we summarize the current experimental detection methods and predictive models for mRNA m5C modifications, focusing on their advantages and limitations. We systematically surveyed the latest research on the effectors related to mRNA m5C modifications and their biological functions in multiple species. Finally, we discuss the physiological effects and pathological significance of m5C modifications in multiple diseases, as well as their therapeutic potential, thereby providing new perspectives for disease treatment and prognosis.
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Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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34
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Manduzio S, Kang H. RNA methylation in chloroplasts or mitochondria in plants. RNA Biol 2021; 18:2127-2135. [PMID: 33779501 PMCID: PMC8632092 DOI: 10.1080/15476286.2021.1909321] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in our understanding of epitranscriptomic RNA methylation have expanded the complexity of gene expression regulation beyond epigenetic regulation involving DNA methylation and histone modifications. The instalment, removal, and interpretation of methylation marks on RNAs are carried out by writers (methyltransferases), erasers (demethylases), and readers (RNA-binding proteins), respectively. Contrary to an emerging body of evidence demonstrating the importance of RNA methylation in the diverse fates of RNA molecules, including splicing, export, translation, and decay in the nucleus and cytoplasm, their roles in plant organelles remain largely unclear and are only now being discovered. In particular, extremely high levels of methylation marks in chloroplast and mitochondrial RNAs suggest that RNA methylation plays essential roles in organellar biogenesis and functions in plants that are crucial for plant development and responses to environmental stimuli. Thus, unveiling the cellular components involved in RNA methylation in cell organelles is essential to better understand plant biology.
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Affiliation(s)
- Stefano Manduzio
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
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35
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Gao S, Sun H, Chen K, Gu X, Chen H, Jiang L, Chen L, Zhang S, Liu Y, Shi D, Liang D, Xu L, Yang J, Ruan Y, Chen H, Shen B, Ma H, Chen YH. Depletion of m 6 A reader protein YTHDC1 induces dilated cardiomyopathy by abnormal splicing of Titin. J Cell Mol Med 2021; 25:10879-10891. [PMID: 34716659 PMCID: PMC8642692 DOI: 10.1111/jcmm.16955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/08/2021] [Accepted: 09/19/2021] [Indexed: 12/01/2022] Open
Abstract
N6 -methyladenosine (m6 A) is the most prevalent modification in mRNA and engages in multiple biological processes. Previous studies indicated that m6 A methyltransferase METTL3 ('writer') and demethylase FTO ('eraser') play critical roles in heart-related disease. However, in the heart, the function of m6 A 'reader', such as YTH (YT521-B homology) domain-containing proteins remains unclear. Here, we report that the defect in YTHDC1 but not other YTH family members contributes to dilated cardiomyopathy (DCM) in mice. Cardiac-specific conditional Ythdc1 knockout led to obvious left ventricular chamber enlargement and severe systolic dysfunction. YTHDC1 deficiency also resulted in the decrease of cardiomyocyte contractility and disordered sarcomere arrangement. By means of integrating multiple high-throughput sequence technologies, including m6 A-MeRIP, RIP-seq and mRNA-seq, we identified 42 transcripts as potential downstream targets of YTHDC1. Amongst them, we found that Titin mRNA was decorated with m6 A modification and depletion of YTHDC1 resulted in aberrant splicing of Titin. Our study suggests that Ythdc1 plays crucial role in regulating the normal contractile function and the development of DCM. These findings clarify the essential role of m6 A reader in cardiac biofunction and provide a novel potential target for the treatment of DCM.
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Affiliation(s)
- Siyun Gao
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haifeng Sun
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing Medical University, Nanjing, China
| | - Kejing Chen
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xueying Gu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing Medical University, Nanjing, China
| | - Hongyu Chen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing Medical University, Nanjing, China
| | - Liudan Jiang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Chen
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shengqi Zhang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Liu
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Dan Shi
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Dandan Liang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Liang Xu
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Jian Yang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Yanjiao Ruan
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Hao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing Medical University, Nanjing, China
| | - Honghui Ma
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China.,Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi-Han Chen
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
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36
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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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37
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Helm M, Schmidt-Dengler MC, Weber M, Motorin Y. General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents. Adv Biol (Weinh) 2021; 5:e2100866. [PMID: 34535986 DOI: 10.1002/adbi.202100866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/09/2021] [Indexed: 12/16/2022]
Abstract
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuing from the application of such chemistries are limited by intrinsic features of chemical reactivity. An important but often ignored fact is that the huge stochiometric excess of unmodified over-modified nucleotides is not inert to any of the reagents employed. Consequently, any reaction aimed at chemical discrimination of modified versus unmodified nucleotides has optimal conditions for selectivity that are ultimately anchored in relative reaction rates, whose ratio imposes intrinsic limits to selectivity. Here chemical reactivities of canonical and modified ribonucleosides are revisited as a basis for an understanding of the limits of selectivity achievable with chemical methods.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Martina C Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, F-54000, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, F-54000, France
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38
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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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39
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Valadon C, Namy O. The Importance of the Epi-Transcriptome in Translation Fidelity. Noncoding RNA 2021; 7:51. [PMID: 34564313 PMCID: PMC8482273 DOI: 10.3390/ncrna7030051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs anticodon-loop, rRNA, and mRNA can affect translation fidelity, and how approaches based on direct manipulations of the level of RNA modification could potentially be used to modulate translation for the treatment of human genetic diseases.
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Affiliation(s)
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France;
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40
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Manavski N, Vicente A, Chi W, Meurer J. The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods. Genes (Basel) 2021; 12:genes12081121. [PMID: 34440296 PMCID: PMC8394491 DOI: 10.3390/genes12081121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.
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Affiliation(s)
- Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Alexandre Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
- Correspondence: ; Tel.: +49-89-218074556
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Parial R, Li H, Li J, Archacki S, Yang Z, Wang IZ, Chen Q, Xu C, Wang QK. Role of epigenetic m 6 A RNA methylation in vascular development: mettl3 regulates vascular development through PHLPP2/mTOR-AKT signaling. FASEB J 2021; 35:e21465. [PMID: 33788967 DOI: 10.1096/fj.202000516rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/11/2022]
Abstract
N6 -methyladenosine (m6A) methylation is the most prevalent RNA modification, and it emerges as an important regulatory mechanism of gene expression involved in many cellular and biological processes. However, the role of m6 A methylation in vascular development is not clear. The m6 A RNA methylation is regulated by dynamic interplay among methyltransferases, binding proteins, and demethylases. Mettl3 is a member of the mettl3-mettl14 methyltransferase complex, referred to as writers that catalyze m6A RNA methylation. Here, we used CRISPR-Cas9 genome editing to develop two lines of knockout (KO) zebrafish for mettl3. Heterozygous mettl3+/- KO embryos show defective vascular development, which is directly visible in fli-EGFP and flk-EGFP zebrafish. Alkaline phosphatase staining and whole mount in situ hybridization with cdh5, and flk markers demonstrated defective development of intersegmental vessels (ISVs), subintestinal vessels (SIVs), interconnecting vessels (ICVs) and dorsal longitudinal anastomotic vessels (DLAV) in both heterozygous mettl3+/- and homozygous mettl3-/- KO zebrafish embryos. Similar phenotypes were observed in zebrafish embryos with morpholino knockdown (KD) of mettl3; however, the vascular defects were rescued fully by overexpression of constitutively active AKT1. KD of METTL3 in human endothelial cells inhibited cell proliferation, migration, and capillary tube formation. Mechanistically, mettl3 KO and KD significantly reduced the levels of m6 A RNA methylation, and AKT phosphorylation (S473) by an increase in the expression of phosphatase enzyme PHLPP2 and reduction in the phosphorylation of mTOR (S2481), a member of the phosphatidylinositol 3-kinase-related kinase family of protein kinases. These data suggest that m6 A RNA methylation regulates vascular development via PHLPP2/mTOR-AKT signaling.
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Affiliation(s)
- Ramendu Parial
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Hui Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jia Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Stephen Archacki
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Zhongcheng Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Isabel Z Wang
- Symbolic Systems Program, Stanford University, Stanford, CA, USA
| | - Qiuyun Chen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Chengqi Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Qing K Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, P.R. China.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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42
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Zong X, Xiao X, Shen B, Jiang Q, Wang H, Lu Z, Wang F, Jin M, Min J, Wang F, Wang Y. The N6-methyladenosine RNA-binding protein YTHDF1 modulates the translation of TRAF6 to mediate the intestinal immune response. Nucleic Acids Res 2021; 49:5537-5552. [PMID: 33999206 PMCID: PMC8191762 DOI: 10.1093/nar/gkab343] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
The intestinal invasion of pathogenic microorganisms can have serious health consequences. Recent evidence has shown that the N6-methyladenosine (m6A) mRNA modification is closely associated with innate immunity; however, the underlying mechanism is poorly understood. Here, we examined the function and mechanism of m6A mRNA modification and the YTH domain-containing protein YTHDF1 (YTH N6-methyladenosine RNA-binding protein 1) in the innate immune response against bacterial pathogens in the intestine. Ribo-seq and m6A-seq analyses revealed that YTHDF1 directs the translation of Traf6 mRNA, which encodes tumor necrosis factor receptor-associated factor 6, thereby regulating the immune response via the m6A modification near the transcript's stop codon. Furthermore, we identified a unique mechanism by which the P/Q/N-rich domain in YTHDF1 interacts with the DEAD domain in the host factor DDX60, thereby regulating the intestinal immune response to bacterial infection by recognizing the target Traf6 transcript. These results provide novel insights into the mechanism by which YTHDF1 recognizes its target and reveal YTHDF1 as an important driver of the intestinal immune response, opening new avenues for developing therapeutic strategies designed to modulate the intestinal immune response to bacterial infection.
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Affiliation(s)
- Xin Zong
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.,The First Affiliated Hospital, School of Public Health, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiao Xiao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hong Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zeqing Lu
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Fengqin Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Mingliang Jin
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Junxia Min
- The First Affiliated Hospital, School of Public Health, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Fudi Wang
- The First Affiliated Hospital, School of Public Health, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Hengyang Medical School, University of South China, Hengyang, China
| | - Yizhen Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
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43
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Li C, Jiang Z, Hao J, Liu D, Hu H, Gao Y, Wang D. Role of N6-methyl-adenosine modification in mammalian embryonic development. Genet Mol Biol 2021; 44:e20200253. [PMID: 33999093 PMCID: PMC8127566 DOI: 10.1590/1678-4685-gmb-2020-0253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 04/07/2021] [Indexed: 11/21/2022] Open
Abstract
N6-methyl-adenosine (m6A) methylation is one of the most common and abundant modifications of RNA molecules in eukaryotes. Although various biological roles of m6A methylation have been elucidated, its role in embryonic development is still unclear. In this review, we focused on the function and expression patterns of m6A-related genes in mammalian embryonic development and the role of m6A modification in the embryonic epigenetic reprogramming process. The modification of m6A is regulated by the combined activities of methyltransferases, demethylases, and m6A-binding proteins. m6A-related genes act synergistically to form a dynamic, reversible m6A pattern, which exists in several physiological processes in various stages of embryonic development. The lack of one of these enzymes affects embryonic m6A levels, leading to abnormal embryonic development and even death. Moreover, m6A is a positive regulator of reprogramming to pluripotency and can affect embryo reprogramming by affecting activation of the maternal-to-zygotic transition. In conclusion, m6A is involved in the regulation of gene expression during embryonic development and the metabolic processes of RNA and plays an important role in the epigenetic modification of embryos.
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Affiliation(s)
- Chengshun Li
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Ziping Jiang
- The First Hospital of Jilin University, Department of hand surgery, Changchun, China
| | - Jindong Hao
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Da Liu
- Changchun University of Chinese Medicine, Department of Pharmacy, Changchun, China
| | - Haobo Hu
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Yan Gao
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Dongxu Wang
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
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44
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Zhang SY, Zhang SW, Tang Y, Fan XN, Meng J. Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation. Bioinformatics 2021; 37:4277-4279. [PMID: 33974000 DOI: 10.1093/bioinformatics/btab362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/20/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION N6-methyladenosine (m6A) is the most abundant mammalian mRNA methylation with versatile functions. To date, although a number of bioinformatics tools have been developed for location discovery of m6A modification, functional understanding is still quite limited. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, there is an urgent need for user-friendly tools to identify and explore the functional relevance of context-specific m6A methylation to gain insights into the epitranscriptome layer of gene expression regulation. RESULTS We introduced here Funm6AViewer, a novel platform to identify, prioritize, and visualize the functional gene interaction networks mediated by dynamic m6A RNA methylation unveiled from a case control study. By taking the differential RNA methylation (DM) data and differential gene expression (DE) data, both of which can be inferred from the widely used MeRIP-seq data, as the inputs, Funm6AViewer enables a series of analysis, including: (1) examining the distribution of differential m6A sites, (2) prioritizing the genes mediated by dynamic m6A methylation, and (3) characterizing functionally the gene regulatory networks mediated by condition-specific m6A RNA methylation. Funm6AViewer should effectively facilitate the understanding of the epitranscriptome circuitry mediated by this reversible RNA modification. Funm6AViewer is available both as a convenient web server (https://www.xjtlu.edu.cn/biologicalsciences/funm6aviewer) with graphical interface and as an independent R package (https://github.com/NWPU-903PR/Funm6AViewer) for local usage. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xı´an 710072, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xı´an 710072, China
| | - Yujiao Tang
- Department of Biological Sciences.,Institute of Integrative Biology, University of Liverpool, Liverpool, L7 8TX, UK
| | - Xiao-Nan Fan
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xı´an 710072, China
| | - Jia Meng
- Department of Biological Sciences.,AI University Center, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, L7 8TX, UK
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45
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He J, Zhou M, Yin J, Wan J, Chu J, Jia J, Sheng J, Wang C, Yin H, He F. METTL3 restrains papillary thyroid cancer progression via m 6A/c-Rel/IL-8-mediated neutrophil infiltration. Mol Ther 2021; 29:1821-1837. [PMID: 33484966 PMCID: PMC8116572 DOI: 10.1016/j.ymthe.2021.01.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 12/15/2020] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
Growing evidence indicates that N6-methyladenosine (m6A) is the most pervasive RNA modification in eukaryotic cells. However, the specific role of METTL3 in papillary thyroid carcinoma (PTC) initiation and development remains elusive. Here we found that downregulation of METTL3 was correlated with malignant progression and poor prognosis in PTC. A variety of gain- and loss-of-function studies clarified the effect of METTL3 on regulation of growth and metastasis of PTC cells in vitro and in vivo. By combining RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (meRIP-seq), our mechanistic studies pinpointed c-Rel and RelA as downstream m6A targets of METTL3. Disruption of METTL3 elicited secretion of interleukin-8 (IL-8), and elevated concentrations of IL-8 promoted recruitment of tumor-associated neutrophils (TANs) in chemotaxis assays and mouse models. Administration of the IL-8 antagonist SB225002 substantially retarded tumor growth and abolished TAN accumulation in immunodeficient mice. Our findings revealed that METTL3 played a pivotal tumor-suppressor role in PTC carcinogenesis through c-Rel and RelA inactivation of the nuclear factor κB (NF-κB) pathway by cooperating with YTHDF2 and altered TAN infiltration to regulate tumor growth, which extends our understanding of the relationship between m6A modification and plasticity of the tumor microenvironment.
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Affiliation(s)
- Jing He
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Mingxia Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jie Yin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Junhu Wan
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jie Chu
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jinlin Jia
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jinxiu Sheng
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chang Wang
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Huiqing Yin
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Fucheng He
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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46
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Wang Y, Zhang L, Ren H, Ma L, Guo J, Mao D, Lu Z, Lu L, Yan D. Role of Hakai in m 6A modification pathway in Drosophila. Nat Commun 2021; 12:2159. [PMID: 33846330 PMCID: PMC8041851 DOI: 10.1038/s41467-021-22424-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/14/2021] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNA, is installed by a multi-component writer complex; however, the exact roles of each component remain poorly understood. Here we show that a potential E3 ubiquitin ligase Hakai colocalizes and interacts with other m6A writer components, and Hakai mutants exhibit typical m6A pathway defects in Drosophila, such as lowered m6A levels in mRNA, aberrant Sxl alternative splicing, wing and behavior defects. Hakai, Vir, Fl(2)d and Flacc form a stable complex, and disruption of either Hakai, Vir or Fl(2)d led to the degradation of the other three components. Furthermore, MeRIP-seq indicates that the effective m6A modification is mostly distributed in 5’ UTRs in Drosophila, in contrast to the mammalian system. Interestingly, we demonstrate that m6A modification is deposited onto the Sxl mRNA in a sex-specific fashion, which depends on the m6A writer. Together, our work not only advances the understanding of mechanism and regulation of the m6A writer complex, but also provides insights into how Sxl cooperate with the m6A pathway to control its own splicing. Drosophila m6A writer complex regulates alternative splicing of the Sex-lethal gene. Here the authors show that a potential E3 ligase Hakai interacts with the fly m6A writer complex and that m6A level is reduced in Hakai mutant flies.
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Affiliation(s)
- Yanhua Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lifeng Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Hang Ren
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lijuan Ma
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Guo
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Decai Mao
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Zhongwen Lu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lijun Lu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Dong Yan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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47
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Lan Q, Liu PY, Bell JL, Wang JY, Hüttelmaier S, Zhang XD, Zhang L, Liu T. The Emerging Roles of RNA m 6A Methylation and Demethylation as Critical Regulators of Tumorigenesis, Drug Sensitivity, and Resistance. Cancer Res 2021; 81:3431-3440. [PMID: 34228629 DOI: 10.1158/0008-5472.can-20-4107] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/12/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022]
Abstract
RNA N6 -methyladenosine (m6A) modification occurs in approximately 25% of mRNAs at the transcriptome-wide level. RNA m6A is regulated by the RNA m6A methyltransferases methyltransferase-like 3 (METTL3), METTL14, and METTL16 (writers), demethylases FTO and ALKBH5 (erasers), and binding proteins YTHDC1-2, YTHDF1-3, IGF2BP1-3, and SND1 (readers). These RNA m6A modification proteins are frequently upregulated or downregulated in human cancer tissues and are often associated with poor patient prognosis. By modulating pre-mRNA splicing, mRNA nuclear export, decay, stability, and translation of oncogenic and tumor suppressive transcripts, RNA m6A modification proteins regulate cancer cell proliferation, survival, migration, invasion, tumor initiation, progression, metastasis, and sensitivity to anticancer therapies. Importantly, small-molecule activators of METTL3, as well as inhibitors of METTL3, FTO, ALKBH5, and IGF2BP1 have recently been identified and have shown considerable anticancer effects when administered alone or in combination with other anticancer agents, both in vitro and in mouse models of human cancers. Future compound screening and design of more potent and selective RNA m6A modification protein inhibitors and activators are expected to provide novel anticancer agents, appropriate for clinical trials in patients with cancer tissues harboring aberrant RNA m6A modification protein expression or RNA m6A modification protein-induced resistance to cancer therapy.
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Affiliation(s)
- Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Pei Y Liu
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Jessica L Bell
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Jenny Y Wang
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University, Halle Saale, Germany
| | - Xu Dong Zhang
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, New South Wales, Australia. .,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China.
| | - Tao Liu
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia. .,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia.,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
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48
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Wang J, Sha Y, Sun T. m 6A Modifications Play Crucial Roles in Glial Cell Development and Brain Tumorigenesis. Front Oncol 2021; 11:611660. [PMID: 33718165 PMCID: PMC7943831 DOI: 10.3389/fonc.2021.611660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/11/2021] [Indexed: 01/27/2023] Open
Abstract
RNA methylation is a reversible post-transcriptional modification to RNA and has a significant impact on numerous biological processes. N6-methyladenosine (m6A) is known as one of the most common types of eukaryotic mRNA methylation modifications, and exists in a wide variety of organisms, including viruses, yeast, plants, mice, and humans. Widespread and dynamic m6A methylation is identified in distinct developmental stages in the brain, and controls development of neural stem cells and their differentiation into neurons, glial cells such as oligodendrocytes and astrocytes. Here we summarize recent advances in our understanding of RNA methylation regulation in brain development, neurogenesis, gliogenesis, and its dysregulation in brain tumors. This review will highlight biological roles of RNA methylation in development and function of neurons and glial cells, and provide insights into brain tumor formation, and diagnostic and treatment strategies.
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Affiliation(s)
- Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China.,College of Materials Science and Engineering, Huaqiao University, Xiamen, China
| | - Yongqiang Sha
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
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49
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Mehdi A, Rabbani SA. Role of Methylation in Pro- and Anti-Cancer Immunity. Cancers (Basel) 2021; 13:cancers13030545. [PMID: 33535484 PMCID: PMC7867049 DOI: 10.3390/cancers13030545] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/09/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
DNA and RNA methylation play a vital role in the transcriptional regulation of various cell types including the differentiation and function of immune cells involved in pro- and anti-cancer immunity. Interactions of tumor and immune cells in the tumor microenvironment (TME) are complex. TME shapes the fate of tumors by modulating the dynamic DNA (and RNA) methylation patterns of these immune cells to alter their differentiation into pro-cancer (e.g., regulatory T cells) or anti-cancer (e.g., CD8+ T cells) cell types. This review considers the role of DNA and RNA methylation in myeloid and lymphoid cells in the activation, differentiation, and function that control the innate and adaptive immune responses in cancer and non-cancer contexts. Understanding the complex transcriptional regulation modulating differentiation and function of immune cells can help identify and validate therapeutic targets aimed at targeting DNA and RNA methylation to reduce cancer-associated morbidity and mortality.
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Affiliation(s)
- Ali Mehdi
- Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Shafaat A. Rabbani
- Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-514-843-1632
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50
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Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A, Soldano A, Roignant JY. Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J 2021; 40:e104975. [PMID: 33428246 PMCID: PMC7883056 DOI: 10.15252/embj.2020104975] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
N6‐methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. This modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior, albeit the underlying molecular mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system, being required to limit axonal growth. Mechanistically, we show that the m6A reader Ythdf directly interacts with Fmr1, the fly homolog of Fragile X mental retardation RNA binding protein (FMRP), to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system and modulates Fmr1 target transcript selection.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hans-Hermann Wessels
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department CIBIO, University of Trento, Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anke Busch
- Bioinformatics Core Facility, IMB, Mainz, Germany
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michela Notarangelo
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Heidelberg-Mannheim, Heidelberg, Germany
| | - Alessandro Quattrone
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessia Soldano
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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