1
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Chen S, Meng J, Zhang Y. Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data. Methods 2024; 228:30-37. [PMID: 38768930 DOI: 10.1016/j.ymeth.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/17/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
With the recent advanced direct RNA sequencing technique that proposed by the Oxford Nanopore Technologies, RNA modifications can be detected and profiled in a simple and straightforward manner. Majority nanopore-based modification studies were devoted to those popular types such as m6A and pseudouridine. To address current limitations on studying the crucial regulator, m1A modification, we conceived this study. We have developed an integrated computational workflow designed for the detection of m1A modifications from direct RNA sequencing data. This workflow comprises a feature extractor responsible for capturing signal characteristics (such as mean, standard deviations, and length of electric signals), a single molecule-level m1A predictor trained with features extracted from the IVT dataset using classical machine learning algorithms, a confident m1A site selector employing the binomial test to identify statistically significant m1A sites, and an m1A modification rate estimator. Our model achieved accurate molecule-level prediction (Average AUC = 0.9689) and reliable m1A site detection and quantification. To show the feasibility of our workflow, we conducted a study on in vivo transcribed human HEK293 cell line, and the results were carefully annotated and compared with other techniques (i.e., Illumina sequencing-based techniques). We believed that this tool will enabling a comprehensive understanding of the m1A modification and its functional mechanisms within cells and organisms.
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Affiliation(s)
- Shenglun Chen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; lnstitute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Wisdom Lake Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Al University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; lnstitute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Yuxin Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; lnstitute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom.
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2
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Yuan W, Zhang R, Lyu H, Xiao S, Guo D, Zhang Q, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies. Cell Death Discov 2024; 10:327. [PMID: 39019857 PMCID: PMC11254935 DOI: 10.1038/s41420-024-02097-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.
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Affiliation(s)
- Wenbin Yuan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Qi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
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3
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Cui J, Sendinc E, Liu Q, Kim S, Fang JY, Gregory RI. m 3C32 tRNA modification controls serine codon-biased mRNA translation, cell cycle, and DNA-damage response. Nat Commun 2024; 15:5775. [PMID: 38982125 PMCID: PMC11233606 DOI: 10.1038/s41467-024-50161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
The epitranscriptome includes a diversity of RNA modifications that influence gene expression. N3-methylcytidine (m3C) mainly occurs in the anticodon loop (position C32) of certain tRNAs yet its role is poorly understood. Here, using HAC-Seq, we report comprehensive METTL2A/2B-, METTL6-, and METTL2A/2B/6-dependent m3C profiles in human cells. METTL2A/2B modifies tRNA-arginine and tRNA-threonine members, whereas METTL6 modifies the tRNA-serine family. However, decreased m3C32 on tRNA-Ser-GCT isodecoders is only observed with combined METTL2A/2B/6 deletion. Ribo-Seq reveals altered translation of genes related to cell cycle and DNA repair pathways in METTL2A/2B/6-deficient cells, and these mRNAs are enriched in AGU codons that require tRNA-Ser-GCT for translation. These results, supported by reporter assays, help explain the observed altered cell cycle, slowed proliferation, and increased cisplatin sensitivity phenotypes of METTL2A/2B/6-deficient cells. Thus, we define METTL2A/2B/6-dependent methylomes and uncover a particular requirement of m3C32 tRNA modification for serine codon-biased mRNA translation of cell cycle, and DNA repair genes.
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Affiliation(s)
- Jia Cui
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Erdem Sendinc
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong Province, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, 510640, Guangzhou, Guangdong Province, China
| | - Sujin Kim
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jaden Y Fang
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Initiative for RNA Medicine, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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4
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Elvira-Blázquez D, Fernández-Justel JM, Arcas A, Statello L, Goñi E, González J, Ricci B, Zaccara S, Raimondi I, Huarte M. YTHDC1 m 6A-dependent and m 6A-independent functions converge to preserve the DNA damage response. EMBO J 2024:10.1038/s44318-024-00153-x. [PMID: 38951610 DOI: 10.1038/s44318-024-00153-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/07/2024] [Accepted: 06/05/2024] [Indexed: 07/03/2024] Open
Abstract
Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identify RNA-binding proteins and modifiers that participate in the p53 response. Among the top hits, we find the m6A reader YTHDC1 as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites of TP53 and other genes involved in the DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency also causes the retention of introns and therefore aberrant protein production of key DNA damage factors. While YTHDC1-mediated intron retention requires m6A, TP53 transcriptional pause-release is promoted by YTHDC1 independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.
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Affiliation(s)
- Daniel Elvira-Blázquez
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - José Miguel Fernández-Justel
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Aida Arcas
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
- Clarivate, Barcelona, Spain
| | - Luisa Statello
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Goñi
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Benedetta Ricci
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara Zaccara
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ivan Raimondi
- New York Genome Center, New York, NY, USA.
- Weill Cornell Medicine, New York, NY, USA.
| | - Maite Huarte
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.
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5
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Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
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Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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6
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The tRNA methyltransferase METTL6 requires seryl-tRNA synthetase for tRNA Ser targeting. Nat Struct Mol Biol 2024:10.1038/s41594-024-01343-1. [PMID: 38918640 DOI: 10.1038/s41594-024-01343-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
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7
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Throll P, G Dolce L, Rico-Lastres P, Arnold K, Tengo L, Basu S, Kaiser S, Schneider R, Kowalinski E. Structural basis of tRNA recognition by the m 3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase. Nat Struct Mol Biol 2024:10.1038/s41594-024-01341-3. [PMID: 38918637 DOI: 10.1038/s41594-024-01341-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Methylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (m3C) is crucial for cellular translation fidelity. Misregulation of the RNA methyltransferases setting this modification can cause aggressive cancers and metabolic disturbances. Here, we report the cryo-electron microscopy structure of the human m3C tRNA methyltransferase METTL6 in complex with seryl-tRNA synthetase (SerRS) and their common substrate tRNASer. Through the complex structure, we identify the tRNA-binding domain of METTL6. We show that SerRS acts as the tRNASer substrate selection factor for METTL6. We demonstrate that SerRS augments the methylation activity of METTL6 and that direct contacts between METTL6 and SerRS are necessary for efficient tRNASer methylation. Finally, on the basis of the structure of METTL6 in complex with SerRS and tRNASer, we postulate a universal tRNA-binding mode for m3C RNA methyltransferases, including METTL2 and METTL8, suggesting that these mammalian paralogs use similar ways to engage their respective tRNA substrates and cofactors.
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Affiliation(s)
| | | | - Palma Rico-Lastres
- Institute of Functional Epigenetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Katharina Arnold
- Institute of Functional Epigenetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Laura Tengo
- European Molecular Biology Laboratory, Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble, France
| | - Stefanie Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Eva Kowalinski
- European Molecular Biology Laboratory, Grenoble, France.
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8
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Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024; 300:107488. [PMID: 38908752 DOI: 10.1016/j.jbc.2024.107488] [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: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to also play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.
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Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
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9
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Wang X, Gan M, Wang Y, Wang S, Lei Y, Wang K, Zhang X, Chen L, Zhao Y, Niu L, Zhang S, Zhu L, Shen L. Comprehensive review on lipid metabolism and RNA methylation: Biological mechanisms, perspectives and challenges. Int J Biol Macromol 2024; 270:132057. [PMID: 38710243 DOI: 10.1016/j.ijbiomac.2024.132057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
Adipose tissue plays a crucial role in maintaining energy balance, regulating hormones, and promoting metabolic health. To address disorders related to obesity and develop effective therapies, it is essential to have a deep understanding of adipose tissue biology. In recent years, RNA methylation has emerged as a significant epigenetic modification involved in various cellular functions and metabolic pathways. Particularly in the realm of adipogenesis and lipid metabolism, extensive research is ongoing to uncover the mechanisms and functional importance of RNA methylation. Increasing evidence suggests that RNA methylation plays a regulatory role in adipocyte development, metabolism, and lipid utilization across different organs. This comprehensive review aims to provide an overview of common RNA methylation modifications, their occurrences, and regulatory mechanisms, focusing specifically on their intricate connections to fat metabolism. Additionally, we discuss the research methodologies used in studying RNA methylation and highlight relevant databases that can aid researchers in this rapidly advancing field.
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Affiliation(s)
- Xingyu Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Saihao Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Lei
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
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10
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Zhou X, Ling Y, Cui J, Wang X, Long N, Teng W, Liu J, Xiang X, Yang H, Chu L. Mitochondrial RNA modification-based signature to predict prognosis of lower grade glioma: a multi-omics exploration and verification study. Sci Rep 2024; 14:12602. [PMID: 38824202 PMCID: PMC11144219 DOI: 10.1038/s41598-024-63592-w] [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: 08/27/2023] [Accepted: 05/30/2024] [Indexed: 06/03/2024] Open
Abstract
Mitochondrial RNA modification (MRM) plays a crucial role in regulating the expression of key mitochondrial genes and promoting tumor metastasis. Despite its significance, comprehensive studies on MRM in lower grade gliomas (LGGs) remain unknown. Single-cell RNA-seq data (GSE89567) was used to evaluate the distribution functional status, and correlation of MRM-related genes in different cell types of LGG microenvironment. We developed an MRM scoring system by selecting potential MRM-related genes using LASSO regression analysis and the Random Survival Forest algorithm, based on multiple bulk RNA-seq datasets from TCGA, CGGA, GSE16011, and E-MTAB-3892. Analysis was performed on prognostic and immunological features, signaling pathways, metabolism, somatic mutations and copy number variations (CNVs), treatment responses, and forecasting of potential small-molecule agents. A total of 35 MRM-related genes were selected from the literature. Differential expression analysis of 1120 normal brain tissues and 529 LGGs revealed that 22 and 10 genes were upregulated and downregulated, respectively. Most genes were associated with prognosis of LGG. METLL8, METLL2A, TRMT112, and METTL2B were extensively expressed in all cell types and different cell cycle of each cell type. Almost all cell types had clusters related to mitochondrial RNA processing, ribosome biogenesis, or oxidative phosphorylation. Cell-cell communication and Pearson correlation analyses indicated that MRM may promoting the development of microenvironment beneficial to malignant progression via modulating NCMA signaling pathway and ICP expression. A total of 11 and 9 MRM-related genes were observed by LASSO and the RSF algorithm, respectively, and finally 6 MRM-related genes were used to establish MRM scoring system (TRMT2B, TRMT11, METTL6, METTL8, TRMT6, and TRUB2). The six MRM-related genes were then validated by qPCR in glioma and normal tissues. MRM score can predict the malignant clinical characteristics, abundance of immune infiltration, gene variation, clinical outcome, the enrichment of signaling pathways and metabolism. In vitro experiments demonstrated that silencing METTL8 significantly curbs glioma cell proliferation and enhances apoptosis. Patients with a high MRM score showed a better response to immunotherapies and small-molecule agents such as arachidonyl trifluoromethyl ketone, MS.275, AH.6809, tacrolimus, and TTNPB. These novel insights into the biological impacts of MRM within the glioma microenvironment underscore its potential as a target for developing precise therapies, including immunotherapeutic approaches.
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Affiliation(s)
- Xingwang Zhou
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Yuanguo Ling
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Junshuan Cui
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Xiang Wang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Niya Long
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Wei Teng
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, People's Republic of China
| | - Xin Xiang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Hua Yang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China.
| | - Liangzhao Chu
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China.
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11
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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12
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Lee BWL, Chuah YH, Yoon J, Grinchuk OV, Liang Y, Hirpara JL, Shen Y, Wang LC, Lim YT, Zhao T, Sobota RM, Yeo TT, Wong ALA, Teo K, Nga VDW, Tan BWQ, Suda T, Toh TB, Pervaiz S, Lin Z, Ong DST. METTL8 links mt-tRNA m 3C modification to the HIF1α/RTK/Akt axis to sustain GBM stemness and tumorigenicity. Cell Death Dis 2024; 15:338. [PMID: 38744809 PMCID: PMC11093979 DOI: 10.1038/s41419-024-06718-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
Epitranscriptomic RNA modifications are crucial for the maintenance of glioma stem cells (GSCs), the most malignant cells in glioblastoma (GBM). 3-methylcytosine (m3C) is a new epitranscriptomic mark on RNAs and METTL8 represents an m3C writer that is dysregulated in cancer. Although METTL8 has an established function in mitochondrial tRNA (mt-tRNA) m3C modification, alternative splicing of METTL8 can also generate isoforms that localize to the nucleolus where they may regulate R-loop formation. The molecular basis for METTL8 dysregulation in GBM, and which METTL8 isoform(s) may influence GBM cell fate and malignancy remain elusive. Here, we investigated the role of METTL8 in regulating GBM stemness and tumorigenicity. In GSC, METTL8 is exclusively localized to the mitochondrial matrix where it installs m3C on mt-tRNAThr/Ser(UCN) for mitochondrial translation and respiration. High expression of METTL8 in GBM is attributed to histone variant H2AZ-mediated chromatin accessibility of HIF1α and portends inferior glioma patient outcome. METTL8 depletion impairs the ability of GSC to self-renew and differentiate, thus retarding tumor growth in an intracranial GBM xenograft model. Interestingly, METTL8 depletion decreases protein levels of HIF1α, which serves as a transcription factor for several receptor tyrosine kinase (RTK) genes, in GSC. Accordingly, METTL8 loss inactivates the RTK/Akt axis leading to heightened sensitivity to Akt inhibitor treatment. These mechanistic findings, along with the intimate link between METTL8 levels and the HIF1α/RTK/Akt axis in glioma patients, guided us to propose a HIF1α/Akt inhibitor combination which potently compromises GSC proliferation/self-renewal in vitro. Thus, METTL8 represents a new GBM dependency that is therapeutically targetable.
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Affiliation(s)
- Bernice Woon Li Lee
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - You Heng Chuah
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jeehyun Yoon
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Oleg V Grinchuk
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yajing Liang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
| | - Jayshree L Hirpara
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yating Shen
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Loo Chien Wang
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tianyun Zhao
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tseng Tsai Yeo
- Department of Surgery, Division of Neurosurgery, National University Hospital, Singapore, Singapore
| | - Andrea Li Ann Wong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
| | - Kejia Teo
- Department of Surgery, Division of Neurosurgery, National University Hospital, Singapore, Singapore
| | - Vincent Diong Weng Nga
- Department of Surgery, Division of Neurosurgery, National University Hospital, Singapore, Singapore
| | - Bryce Wei Quan Tan
- Department of Medicine, National University Hospital, Singapore, Singapore
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Tan Boon Toh
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhewang Lin
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- National Neuroscience Institute, 308433, Singapore, Singapore.
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13
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Zeng Z, Zou Y, Cai W, Lin FC, Wang H. Roles of CcDFR and CcOMT9 in the cyanidin biosynthesis and development of Cordyceps cicadae. Front Microbiol 2024; 15:1353710. [PMID: 38511011 PMCID: PMC10953825 DOI: 10.3389/fmicb.2024.1353710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Cordyceps cicadae is a traditional Chinese medicinal fungus known for its rich production of bioactive substances, particularly cyanidin, an anthocyanin commonly found in plants with notable anti-inflammatory, anti-tumor, antiviral, and antibacterial properties. This study revealed two key genes, CcDFR and CcOMT9, affecting cyanidin biosynthesis in C. cicadae. Methods The roles of these genes in cyanidin production, growth, and development were elucidated through the gene knockout method, phenotypic analysis, transcriptomics, and metabolomics. Results CcDFR deletion led to reduced cyanidin-3-O-glucoside (C3G), suppressed expression of cyanidin biosynthesis genes, impaired synnemata formation, decreased polysaccharide and adenosine content, and diminished chitinase activity. Meanwhile, the ΔCcOMT9 mutant exhibited an increase in C3G production, promoted expression of cyanidin biosynthesis genes and rising bioactive compounds, suppressed RNA methylation, and led to phenylalanine accumulation with no effect on fruiting body formation. Discussion We revealed a distinct anthocyanin biosynthesis pathway in C. cicadae and identified two genes with opposite functions, laying the foundation for future genetic modification of cyanidin-producing strains using modern biological techniques. This will shorten the production period of this valuable compound, facilitating the industrial-scale production of cyanidin.
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Affiliation(s)
- Zixuan Zeng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Zou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Weiming Cai
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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14
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Añazco-Guenkova AM, Miguel-López B, Monteagudo-García Ó, García-Vílchez R, Blanco S. The impact of tRNA modifications on translation in cancer: identifying novel therapeutic avenues. NAR Cancer 2024; 6:zcae012. [PMID: 38476632 PMCID: PMC10928989 DOI: 10.1093/narcan/zcae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Recent advancements have illuminated the critical role of RNA modifications in post-transcriptional regulation, shaping the landscape of gene expression. This review explores how tRNA modifications emerge as critical players, fine-tuning functionalities that not only maintain the fidelity of protein synthesis but also dictate gene expression and translation profiles. Highlighting their dysregulation as a common denominator in various cancers, we systematically investigate the intersection of both cytosolic and mitochondrial tRNA modifications with cancer biology. These modifications impact key processes such as cell proliferation, tumorigenesis, migration, metastasis, bioenergetics and the modulation of the tumor immune microenvironment. The recurrence of altered tRNA modification patterns across different cancer types underscores their significance in cancer development, proposing them as potential biomarkers and as actionable targets to disrupt tumorigenic processes, offering new avenues for precision medicine in the battle against cancer.
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Affiliation(s)
- Ana M Añazco-Guenkova
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Óscar Monteagudo-García
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
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15
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Hou Y, Zhang W, McGilvray PT, Sobczyk M, Wang T, Weng SHS, Huff A, Huang S, Pena N, Katanski CD, Pan T. Engineered mischarged transfer RNAs for correcting pathogenic missense mutations. Mol Ther 2024; 32:352-371. [PMID: 38104240 PMCID: PMC10861979 DOI: 10.1016/j.ymthe.2023.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023] Open
Abstract
Missense mutations account for approximately 50% of pathogenic mutations in human genetic diseases, and most lack effective treatments. Gene therapies, gene editing, and RNA therapies, including transfer RNA (tRNA) modalities, are common strategies for genetic disease treatments. However, reported tRNA therapies are for nonsense mutations only. It has not been explored how tRNAs can be engineered to correct missense mutations. Here, we describe missense-correcting tRNAs (mc-tRNAs) as a potential therapeutic for correcting pathogenic missense mutations. Mc-tRNAs are engineered tRNAs charged with one amino acid, but read codons of another in translation. We first developed a series of fluorescent protein-based reporters that indicate the successful correction of missense mutations via restoration of fluorescence. We engineered mc-tRNAs that effectively corrected serine and arginine missense mutations in the reporters and confirmed the amino acid substitution by mass spectrometry and mc-tRNA expression by sequencing. We examined the transcriptome response to mc-tRNA expression and found some mc-tRNAs induced minimum transcriptomic changes. Furthermore, we applied an mc-tRNA to rescue a pathogenic CAPN3 Arg-to-Gln mutant involved in LGMD2A. These results establish a versatile pipeline for mc-tRNA engineering and demonstrate the potential of mc-tRNA as an alternative therapeutic platform for the treatment of genetic disorders.
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Affiliation(s)
- Yichen Hou
- Committee on Genomics, Genetics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Marek Sobczyk
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tianxin Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Allen Huff
- Proteomics Platform, University of Chicago, Chicago, IL 60637, USA
| | - Sihao Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Noah Pena
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
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16
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Zhang F, Ignatova VV, Ming GL, Song H. Advances in brain epitranscriptomics research and translational opportunities. Mol Psychiatry 2024; 29:449-463. [PMID: 38123727 PMCID: PMC11116067 DOI: 10.1038/s41380-023-02339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Various chemical modifications of all RNA transcripts, or epitranscriptomics, have emerged as crucial regulators of RNA metabolism, attracting significant interest from both basic and clinical researchers due to their diverse functions in biological processes and immense clinical potential as highlighted by the recent profound success of RNA modifications in improving COVID-19 mRNA vaccines. Rapid accumulation of evidence underscores the critical involvement of various RNA modifications in governing normal neural development and brain functions as well as pathogenesis of brain disorders. Here we provide an overview of RNA modifications and recent advancements in epitranscriptomic studies utilizing animal models to elucidate important roles of RNA modifications in regulating mammalian neurogenesis, gliogenesis, synaptic formation, and brain function. Moreover, we emphasize the pivotal involvement of RNA modifications and their regulators in the pathogenesis of various human brain disorders, encompassing neurodevelopmental disorders, brain tumors, psychiatric and neurodegenerative disorders. Furthermore, we discuss potential translational opportunities afforded by RNA modifications in combatting brain disorders, including their use as biomarkers, in the development of drugs or gene therapies targeting epitranscriptomic pathways, and in applications for mRNA-based vaccines and therapies. We also address current limitations and challenges hindering the widespread clinical application of epitranscriptomic research, along with the improvements necessary for future progress.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valentina V Ignatova
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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17
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Dulic M, Godinic-Mikulcic V, Kekez M, Evic V, Rokov-Plavec J. Protein-Protein Interactions of Seryl-tRNA Synthetases with Emphasis on Human Counterparts and Their Connection to Health and Disease. Life (Basel) 2024; 14:124. [PMID: 38255739 PMCID: PMC10817482 DOI: 10.3390/life14010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Seryl-tRNA synthetases (SerRSs), members of the aminoacyl-tRNA synthetase family, interact with diverse proteins, enabling SerRSs to enhance their role in the translation of the genetic message or to perform alternative functions in cellular processes beyond translation. Atypical archaeal SerRS interacts with arginyl-tRNA synthetase and proteins of the ribosomal P-stalk to optimize translation through tRNA channeling. The complex between yeast SerRS and peroxin Pex21p provides a connection between translation and peroxisome function. The partnership between Arabidopsis SerRS and BEN1 indicates a link between translation and brassinosteroid metabolism and may be relevant in plant stress response mechanisms. In Drosophila, the unusual heterodimeric mitochondrial SerRS coordinates mitochondrial translation and replication via interaction with LON protease. Evolutionarily conserved interactions of yeast and human SerRSs with m3C32 tRNA methyltransferases indicate coordination between tRNA modification and aminoacylation in the cytosol and mitochondria. Human cytosolic SerRS is a cellular hub protein connecting translation to vascular development, angiogenesis, lipogenesis, and telomere maintenance. When translocated to the nucleus, SerRS acts as a master negative regulator of VEGFA gene expression. SerRS alone or in complex with YY1 and SIRT2 competes with activating transcription factors NFκB1 and c-Myc, resulting in balanced VEGFA expression important for proper vascular development and angiogenesis. In hypoxia, SerRS phosphorylation diminishes its binding to the VEGFA promoter, while the lack of nutrients triggers SerRS glycosylation, reducing its nuclear localization. Additionally, SerRS binds telomeric DNA and cooperates with the shelterin protein POT1 to regulate telomere length and cellular senescence. As an antitumor and antiangiogenic factor, human cytosolic SerRS appears to be a promising drug target and therapeutic agent for treating cancer, cardiovascular diseases, and possibly obesity and aging.
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Affiliation(s)
| | | | | | | | - Jasmina Rokov-Plavec
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia; (M.D.); (V.G.-M.); (M.K.); (V.E.)
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18
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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19
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Hehenberger E, Guo J, Wilken S, Hoadley K, Sudek L, Poirier C, Dannebaum R, Susko E, Worden AZ. Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias. Mol Biol Evol 2023; 40:msad251. [PMID: 37987557 PMCID: PMC10735309 DOI: 10.1093/molbev/msad251] [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: 04/17/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in "light stress." The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.
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Affiliation(s)
- Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, CZ
| | - Jian Guo
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susanne Wilken
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kenneth Hoadley
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Lisa Sudek
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Richard Dannebaum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, CA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Max Planck Institute for Evolutionary Biology, 24306 Plön, DE
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20
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Jia W, Yuan J, Li S, Cheng B. The role of dysregulated mRNA translation machinery in cancer pathogenesis and therapeutic value of ribosome-inactivating proteins. Biochim Biophys Acta Rev Cancer 2023; 1878:189018. [PMID: 37944831 DOI: 10.1016/j.bbcan.2023.189018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Dysregulated protein synthesis is a hallmark of tumors. mRNA translation reprogramming contributes to tumorigenesis, which is fueled by abnormalities in ribosome formation, tRNA abundance and modification, and translation factors. Not only malignant cells but also stromal cells within tumor microenvironment can undergo transformation toward tumorigenic phenotypes during translational reprogramming. Ribosome-inactivating proteins (RIPs) have garnered interests for their ability to selectively inhibit protein synthesis and suppress tumor growth. This review summarizes the role of dysregulated translation machinery in tumor development and explores the potential of RIPs in cancer treatment.
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Affiliation(s)
- Wentao Jia
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China
| | - Jiaying Yuan
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Shu Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, China.
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China.
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21
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Li L, Tang C, Ye J, Xu D, Chu C, Wang L, Zhou Q, Gan S, Liu B. Bioinformatic analysis of m6A "reader" YTH family in pan-cancer as a clinical prognosis biomarker. Sci Rep 2023; 13:17350. [PMID: 37833468 PMCID: PMC10575994 DOI: 10.1038/s41598-023-44143-1] [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: 05/05/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
The m6A methylation of mRNA has been demonstrated to interact with the "Reader". YTH domain family is one of the readers containing five members involved in the progression of multiple tumors. The present study aimed to explore the YTH family's role in seventeen cancer types. Data were downloaded from The Cancer Genome Atlas (TCGA) dataset and analyzed by Software R 3.6.3. Using different bioinformatics methods, including analyses of the overall survival (OS) and disease-free survival (DFS), Gene Set Variation Analysis (GSVA) enrichment. Genomics of Drug Sensitivity in Cancer (GDSC), CIBERSORT algorithm, multivariate and lasso cox regression analysis our results reveal that, while the expression of the YTH domain family varies distinctively in different cancer types the expression of YTH family is upregulated in most cancer types, especially in liver cancer, and the liver cancer prediction model established herein includes YTHDF1 and YTHDF2. Therefore, the results of the present study have demonstrated that the YTH domain family has the potential to predict the prognosis of cancer and the sensitivity to immunotherapy.
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Affiliation(s)
- Lin Li
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Chao Tang
- National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Road, Hangzhou, 310052, China.
| | - Jianqing Ye
- Department of Urology, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Da Xu
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Chuanmin Chu
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Lei Wang
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Qiwei Zhou
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Sishun Gan
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Bing Liu
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China.
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22
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Hogan CA, Gratz SJ, Dumouchel JL, Thakur RS, Delgado A, Lentini JM, Madhwani KR, Fu D, O'Connor‐Giles KM. Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function. EMBO Rep 2023; 24:e56808. [PMID: 37642556 PMCID: PMC10561368 DOI: 10.15252/embr.202356808] [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: 01/11/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Nervous system function rests on the formation of functional synapses between neurons. We have identified TRMT9B as a new regulator of synapse formation and function in Drosophila. TRMT9B has been studied for its role as a tumor suppressor and is one of two metazoan homologs of yeast tRNA methyltransferase 9 (Trm9), which methylates tRNA wobble uridines. Whereas Trm9 homolog ALKBH8 is ubiquitously expressed, TRMT9B is enriched in the nervous system. However, in the absence of animal models, TRMT9B's role in the nervous system has remained unstudied. Here, we generate null alleles of TRMT9B and find it acts postsynaptically to regulate synaptogenesis and promote neurotransmission. Through liquid chromatography-mass spectrometry, we find that ALKBH8 catalyzes canonical tRNA wobble uridine methylation, raising the question of whether TRMT9B is a methyltransferase. Structural modeling studies suggest TRMT9B retains methyltransferase function and, in vivo, disruption of key methyltransferase residues blocks TRMT9B's ability to rescue synaptic overgrowth, but not neurotransmitter release. These findings reveal distinct roles for TRMT9B in the nervous system and highlight the significance of tRNA methyltransferase family diversification in metazoans.
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Affiliation(s)
- Caley A Hogan
- Genetics Training ProgramUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Scott J Gratz
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | | | - Rajan S Thakur
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | - Ambar Delgado
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | - Jenna M Lentini
- Department of Biology, Center for RNA BiologyUniversity of RochesterRochesterNYUSA
| | | | - Dragony Fu
- Department of Biology, Center for RNA BiologyUniversity of RochesterRochesterNYUSA
| | - Kate M O'Connor‐Giles
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
- Carney Institute for Brain ScienceProvidenceRIUSA
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23
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Huang MH, Wang JT, Zhang JH, Mao XL, Peng GX, Lin X, Lv D, Yuan C, Lin H, Wang ED, Zhou XL. Mitochondrial RNA m 3C methyltransferase METTL8 relies on an isoform-specific N-terminal extension and modifies multiple heterogenous tRNAs. Sci Bull (Beijing) 2023; 68:2094-2105. [PMID: 37573249 DOI: 10.1016/j.scib.2023.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 08/14/2023]
Abstract
Methyltransferase-like 8 (METTL8) encodes a mitochondria-localized METTL8-Iso1 and a nucleolus-distributed METTL8-Iso4 isoform, which differ only in their N-terminal extension (N-extension), by mRNA alternative splicing. METTL8-Iso1 generates 3-methylcytidine at position 32 (m3C32) of mitochondrial tRNAThr and tRNASer(UCN). Whether METTL8-Iso4 is an active m3C32 methyltransferase and the role of the N-extension in mitochondrial tRNA m3C32 formation remain unclear. Here, we revealed that METTL8-Iso4 was inactive in m3C32 generation due to the lack of N-extension, which contains several absolutely conserved modification-critical residues; the counterparts were likewise essential in cytoplasmic m3C32 biogenesis by methyltransferase-like 2A (METTL2A) or budding yeasts tRNA N3-methylcytidine methyltransferase (Trm140), in vitro and in vivo. Cross-compartment/species tRNA modification assays unexpectedly found that METTL8-Iso1 efficiently introduced m3C32 to several cytoplasmic or even bacterial tRNAs in vitro. m3C32 did not influence tRNAThrN6-threonylcarbamoyladenosine (t6A) modification or aminoacylation. In addition to its interaction with mitochondrial seryl-tRNA synthetase (SARS2), we further discovered an interaction between mitochondrial threonyl-tRNA synthetase (TARS2) and METTL8-Iso1. METTL8-Iso1 substantially stimulated the aminoacylation activities of SARS2 and TARS2 in vitro, suggesting a functional connection between mitochondrial tRNA modification and charging. Altogether, our results deepen the mechanistic insights into mitochondrial m3C32 biogenesis and provide a valuable route to prepare cytoplasmic/bacterial tRNAs with only a m3C32 moiety, aiding in future efforts to investigate its effects on tRNA structure and function.
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Affiliation(s)
- Meng-Han Huang
- Key Laboratory of RNA Science and Engineering, 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
| | - Jin-Tao Wang
- Key Laboratory of RNA Science and Engineering, 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
| | - Jian-Hui Zhang
- Key Laboratory of RNA Science and Engineering, 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; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xue-Ling Mao
- Key Laboratory of RNA Science and Engineering, 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
| | - Gui-Xin Peng
- Key Laboratory of RNA Science and Engineering, 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
| | - Xiuying Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; School of Life Sciences, Hainan University, Haikou 570228, China
| | - Daizhu Lv
- Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chen Yuan
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Huan Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, 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.
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, 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; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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24
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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25
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Liu S, He L, Bannister OB, Li J, Schnegelberger RD, Vanderpuye CM, Althouse AD, Schopfer FJ, Wahlang B, Cave MC, Monga SP, Zhang X, Arteel GE, Beier JI. Western diet unmasks transient low-level vinyl chloride-induced tumorigenesis; potential role of the (epi-)transcriptome. Toxicol Appl Pharmacol 2023; 468:116514. [PMID: 37061008 PMCID: PMC10164119 DOI: 10.1016/j.taap.2023.116514] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
BACKGROUND & AIMS Vinyl chloride (VC) monomer is a volatile organic compound commonly used in industry. At high exposure levels, VC causes liver cancer and toxicant-associated steatohepatitis. However, lower exposure levels (i.e., sub-regulatory exposure limits) that do not directly damage the liver, enhance injury caused by Western diet (WD). It is still unknown if the long-term impact of transient low-concentration VC enhances the risk of liver cancer development. This is especially a concern given that fatty liver disease is in and of itself a risk factor for the development of liver cancer. METHODS C57Bl/6 J mice were fed WD or control diet (CD) for 1 year. During the first 12 weeks of feeding only, mice were also exposed to VC via inhalation at sub-regulatory limit concentrations (<1 ppm) or air for 6 h/day, 5 days/week. RESULTS Feeding WD for 1 year caused significant hepatic injury, which was exacerbated by VC. Additionally, VC increased the number of tumors which ranged from moderately to poorly differentiated hepatocellular carcinoma (HCC). Transcriptomic analysis demonstrated VC-induced changes in metabolic but also ribosomal processes. Epitranscriptomic analysis showed a VC-induced shift of the modification pattern that has been associated with metabolic disease, mitochondrial dysfunction, and cancer. CONCLUSIONS These data indicate that VC sensitizes the liver to other stressors (e.g., WD), resulting in enhanced tumorigenesis. These data raise concerns about potential interactions between VC exposure and WD. It also emphasizes that current safety restrictions may be insufficient to account for other factors that can influence hepatotoxicity.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh, United States of America; Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America.
| | - Liqing He
- Department of Chemistry, University of Louisville, Louisville, KY 40208, United States of America.
| | - Olivia B Bannister
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Jiang Li
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Regina D Schnegelberger
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, United States of America.
| | - Charis-Marie Vanderpuye
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Andrew D Althouse
- Division of General Internal Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
| | - Francisco J Schopfer
- Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Pharmacology and Chemical Biology, University of Pittsburgh, United States of America.
| | - Banrida Wahlang
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Superfund Research Center, University of Louisville, Louisville, KY 40202, United States of America; Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40202, United States of America; Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY 40202, United States of America; University of Louisville Alcohol Research Center, Louisville, KY 40202, United States of America.
| | - Matthew C Cave
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Superfund Research Center, University of Louisville, Louisville, KY 40202, United States of America; Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40202, United States of America; Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY 40202, United States of America; University of Louisville Alcohol Research Center, Louisville, KY 40202, United States of America; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Liver Transplant Program at UofL Health-Jewish Hospital Trager Transplant Center, Louisville, KY 40202, United States of America; The Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, United States of America.
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh, United States of America; Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40208, United States of America; Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40202, United States of America; Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY 40202, United States of America; University of Louisville Alcohol Research Center, Louisville, KY 40202, United States of America.
| | - Gavin E Arteel
- Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Environmental and Occupational Health University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
| | - Juliane I Beier
- Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America; Department of Environmental and Occupational Health University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
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26
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Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. THE PLANT CELL 2023; 35:1801-1816. [PMID: 36794718 PMCID: PMC10226571 DOI: 10.1093/plcell/koad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 05/30/2023]
Abstract
Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Diep R Ganguly
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
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27
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Jones JD, Franco MK, Smith TJ, Snyder LR, Anders AG, Ruotolo BT, Kennedy RT, Koutmou KS. Methylated guanosine and uridine modifications in S. cerevisiae mRNAs modulate translation elongation. RSC Chem Biol 2023; 4:363-378. [PMID: 37181630 PMCID: PMC10170649 DOI: 10.1039/d2cb00229a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/15/2023] [Indexed: 02/22/2023] Open
Abstract
Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Tyler J Smith
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Laura R Snyder
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Anna G Anders
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
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28
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Mohl DA, Lagies S, Zodel K, Zumkeller M, Peighambari A, Ganner A, Plattner DA, Neumann-Haefelin E, Adlesic M, Frew IJ, Kammerer B. Integrated Metabolomic and Transcriptomic Analysis of Modified Nucleosides for Biomarker Discovery in Clear Cell Renal Cell Carcinoma. Cells 2023; 12:cells12081102. [PMID: 37190010 DOI: 10.3390/cells12081102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers. The biallelic inactivation of the von Hippel-Lindau tumor suppressor gene (VHL) is the truncal driver mutation of most cases of ccRCC. Cancer cells are metabolically reprogrammed and excrete modified nucleosides in larger amounts due to their increased RNA turnover. Modified nucleosides occur in RNAs and cannot be recycled by salvage pathways. Their potential as biomarkers has been demonstrated for breast or pancreatic cancer. To assess their suitability as biomarkers in ccRCC, we used an established murine ccRCC model, harboring Vhl, Trp53 and Rb1 (VPR) knockouts. Cell culture media of this ccRCC model and primary murine proximal tubular epithelial cells (PECs) were investigated by HPLC coupled to triple-quadrupole mass spectrometry using multiple-reaction monitoring. VPR cell lines were significantly distinguishable from PEC cell lines and excreted higher amounts of modified nucleosides such as pseudouridine, 5-methylcytidine or 2'-O-methylcytidine. The method's reliability was confirmed in serum-starved VPR cells. RNA-sequencing revealed the upregulation of specific enzymes responsible for the formation of those modified nucleosides in the ccRCC model. These enzymes included Nsun2, Nsun5, Pus1, Pus7, Naf1 and Fbl. In this study, we identified potential biomarkers for ccRCC for validation in clinical trials.
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Affiliation(s)
- Daniel A Mohl
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Lagies
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Kyra Zodel
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Matthias Zumkeller
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Asin Peighambari
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Athina Ganner
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Dietmar A Plattner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mojca Adlesic
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Ian J Frew
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Signalling Research Centre BIOSS, University of Freiburg, 79104 Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Bernd Kammerer
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centre BIOSS, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
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Hao L, Zhang J, Liu Z, Lin X, Guo J. Epitranscriptomics in the development, functions, and disorders of cancer stem cells. Front Oncol 2023; 13:1145766. [PMID: 37007137 PMCID: PMC10063963 DOI: 10.3389/fonc.2023.1145766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/10/2023] [Indexed: 03/19/2023] Open
Abstract
Biomolecular modifications play an important role in the development of life, and previous studies have investigated the role of DNA and proteins. In the last decade, with the development of sequencing technology, the veil of epitranscriptomics has been gradually lifted. Transcriptomics focuses on RNA modifications that affect gene expression at the transcriptional level. With further research, scientists have found that changes in RNA modification proteins are closely linked to cancer tumorigenesis, progression, metastasis, and drug resistance. Cancer stem cells (CSCs) are considered powerful drivers of tumorigenesis and key factors for therapeutic resistance. In this article, we focus on describing RNA modifications associated with CSCs and summarize the associated research progress. The aim of this review is to identify new directions for cancer diagnosis and targeted therapy.
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Affiliation(s)
- Linlin Hao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Jian Zhang
- School of Life Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhongshan Liu
- Department of Tumor Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Xia Lin
- Department of Tumor Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Jie Guo
- Department of Tumor Radiotherapy, The Second Hospital of Jilin University, Changchun, China
- *Correspondence: Jie Guo,
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30
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Zhang F, Yoon K, Zhang DY, Kim NS, Ming GL, Song H. Epitranscriptomic regulation of cortical neurogenesis via Mettl8-dependent mitochondrial tRNA m 3C modification. Cell Stem Cell 2023; 30:300-311.e11. [PMID: 36764294 PMCID: PMC10031801 DOI: 10.1016/j.stem.2023.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/07/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023]
Abstract
Increasing evidence implicates the critical roles of various epitranscriptomic RNA modifications in different biological processes. Methyltransferase METTL8 installs 3-methylcytosine (m3C) modification of mitochondrial tRNAs in vitro; however, its role in intact biological systems is unknown. Here, we show that Mettl8 is localized in mitochondria and installs m3C specifically on mitochondrial tRNAThr/Ser(UCN) in mouse embryonic cortical neural stem cells. At molecular and cellular levels, Mettl8 deletion in cortical neural stem cells leads to reduced mitochondrial protein translation and attenuated respiration activity. At the functional level, conditional Mettl8 deletion in mice results in impaired embryonic cortical neural stem cell maintenance in vivo, which can be rescued by pharmacologically enhancing mitochondrial functions. Similarly, METTL8 promotes mitochondrial protein expression and neural stem cell maintenance in human forebrain cortical organoids. Together, our study reveals a conserved epitranscriptomic mechanism of Mettl8 and mitochondrial tRNA m3C modification in maintaining embryonic cortical neural stem cells in mice and humans.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kijun Yoon
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Y Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nam-Shik Kim
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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31
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Sarraf G, Chhabra R. Emerging role of mRNA methylation in regulating the hallmarks of cancer. Biochimie 2023; 206:61-72. [PMID: 36244577 DOI: 10.1016/j.biochi.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/29/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
Abstract
The dynamic chemical modifications of DNA, RNA, and proteins can transform normal cells into malignant ones. While the DNA and protein modifications in cancer have been described extensively in the literature, there are fewer reports about the role of RNA modifications in cancer. There are over 100 forms of RNA modifications and one of these, mRNA methylation, plays a critical role in the malignant properties of the cells. mRNA methylation is a reversible modification responsible for regulating protein expression at the post-transcriptional level. Despite being discovered in the 1970s, a complete understanding of the different proteins involved and the mechanism behind mRNA methylation remains largely unknown. However, these mRNA methylations have been shown to foster cancer hallmarks via specific cellular targets inside the cell. In this review, we provide a brief overview of mRNA methylation and its emerging role in regulating the various hallmarks of cancer.
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Affiliation(s)
- Gargi Sarraf
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
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Integrated investigation of the clinical implications and targeted landscape for RNA methylation modifications in hepatocellular carcinoma. Eur J Med Res 2023; 28:46. [PMID: 36707911 PMCID: PMC9881284 DOI: 10.1186/s40001-023-01016-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND RNA methylation (RM) is a crucial post-translational modification (PTM) that directs epigenetic regulation. It mostly consists of N1-methyladenosine (m1A), 5-methylcytosine (m5C), N3-methylcytidine (m3C), N6-methyladenosine (m6A), and 2'-O-methylation (Nm). The "writers" mainly act as intermediaries between these modifications and associated biological processes. However, little is known about the interactions and potential functions of these RM writers in hepatocellular carcinoma (HCC). METHODS The expression properties and genetic alterations of 38 RM writers were assessed in HCC samples from five bioinformatic datasets. Two patterns associated with RM writers were identified using consensus clustering. Then, utilizing differentially expressed genes (DEGs) from different RM subtypes, we built a risk model called RM_Score. Additionally, we investigated the correlation of RM_Score with clinical characteristics, tumor microenvironment (TME) infiltration, molecular subtypes, therapeutic response, immunotherapy effectiveness, and competing endogenous RNA (ceRNA) network. RESULTS RM writers were correlated with TME cell infiltration and prognosis. Cluster_1/2 and gene.cluster_A/B were shown to be capable of distinguishing the HCC patients with poor prognosis after consensus and unsupervised clustering of RNA methylation writers. Additionally, we constructed RNA modification pattern-specific risk model and subdivided the cases into RM_Score high and RM_Score low subgroups. In individual cohorts or merged datasets, the high RM_Score was related to a worse overall survival of HCC patients. RM_Score also exhibited correlations with immune and proliferation related pathways. In response to anti-cancer treatments, the RM_Score had a negative correlation (drug sensitive) with drugs that focused on the MAPK/ERK and metabolism signaling, and a positive correlation (drug resistant) with compounds targeting RKT and PI3K/mTOR signaling pathway. Notably, the RM_Score was connected to the therapeutic effectiveness of PD-L1 blockage, implying that RM writers may be the target of immunotherapy to optimize clinical outcomes. Additionally, a ceRNA network was generated including 2 lncRNAs, 4 miRNAs, and 7 mRNAs that was connected to RM writers. CONCLUSIONS We thoroughly investigated the potential functions of RNA methylation writers and established an RM_patterns-based risk model for HCC patients. This study emphasized the critical functions of RM modification in TME infiltration, targeted therapy, and immunotherapy, providing potential targets for HCC.
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The Repertoire of RNA Modifications Orchestrates a Plethora of Cellular Responses. Int J Mol Sci 2023; 24:ijms24032387. [PMID: 36768716 PMCID: PMC9916637 DOI: 10.3390/ijms24032387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Although a plethora of DNA modifications have been extensively investigated in the last decade, recent breakthroughs in molecular biology, including high throughput sequencing techniques, have enabled the identification of post-transcriptional marks that decorate RNAs; hence, epitranscriptomics has arisen. This recent scientific field aims to decode the regulatory layer of the transcriptome and set the ground for the detection of modifications in ribose nucleotides. Until now, more than 170 RNA modifications have been reported in diverse types of RNA that contribute to various biological processes, such as RNA biogenesis, stability, and transcriptional and translational accuracy. However, dysfunctions in the RNA-modifying enzymes that regulate their dynamic level can lead to human diseases and cancer. The present review aims to highlight the epitranscriptomic landscape in human RNAs and match the catalytic proteins with the deposition or deletion of a specific mark. In the current review, the most abundant RNA modifications, such as N6-methyladenosine (m6A), N5-methylcytosine (m5C), pseudouridine (Ψ) and inosine (I), are thoroughly described, their functional and regulatory roles are discussed and their contributions to cellular homeostasis are stated. Ultimately, the involvement of the RNA modifications and their writers, erasers, and readers in human diseases and cancer is also discussed.
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Zhang R, Xia Y, Dong J, Ju X, Zhou K, Cao X, Li J, Ru J, Guo M, Zhang S. Comprehensive Analysis of m7G-Related Genes and Chronic Hepatitis B: Diagnostic Markers, Immune Microenvironment Regulation, Disease Progression. J Immunol Res 2023; 2023:9471520. [PMID: 37206976 PMCID: PMC10191754 DOI: 10.1155/2023/9471520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Chronic hepatitis B (CHB) is a major public health problem in the world. It is the main cause of liver cirrhosis and liver cancer. Although many important roles of RNA modification in stem cells or tumor diseases have been identified, the role of N7-methylguanosine (m7G) modification in the process of chronic HBV infection has not been clearly defined. Therefore, we conducted a systematic analysis on the process of chronic HBV infection. We found that a total of 18 m7G-related genes were altered in chronic HBV infection, and then we screened out CHB potential diagnostic biomarkers using machine learning and random forest methods. RT-qPCR was performed on the samples of healthy people and CHB, which further verified the possibility of being a diagnostic marker. Then, we typed CHB patients based on these 18 genes. We found that the immune microenvironment of different subtypes was different. Among them, patients with subtype-Ⅰ had severe immune response, that is, relatively serious immune cell infiltration, rich immune pathways, relatively many HLA genes, and immune checkpoints. Finally, we conducted an in-depth discussion on our m7G-related genes, and found that m7G gene related to immune cell infiltration may be involved in the disease progression of CHB patients, which was also confirmed in the GSE84044 dataset. In conclusion, m7G-related genes can not only serve as diagnostic markers of CHB, but also participate in the regulation of immune microenvironment and play an important role in the progression of CHB.
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Affiliation(s)
- Rongzheng Zhang
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yan Xia
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianming Dong
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaomei Ju
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kun Zhou
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Clinical Laboratory, Beidahuang Industry Group General Hospital, Harbin, China
| | - Xinyang Cao
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaqi Li
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaqiu Ru
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Mengrui Guo
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuyun Zhang
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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35
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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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Abstract
The methyltransferase-like (METTL) family is a diverse group of methyltransferases that can methylate nucleotides, proteins, and small molecules. Despite this diverse array of substrates, they all share a characteristic seven-beta-strand catalytic domain, and recent evidence suggests many also share an important role in stem cell biology. The most well characterized family members METTL3 and METTL14 dimerize to form an N6-methyladenosine (m6A) RNA methyltransferase with established roles in cancer progression. However, new mouse models indicate that METTL3/METTL14 are also important for embryonic stem cell (ESC) development and postnatal hematopoietic and neural stem cell self-renewal and differentiation. METTL1, METTL5, METTL6, METTL8, and METTL17 also have recently identified roles in ESC pluripotency and differentiation, while METTL11A/11B, METTL4, METTL7A, and METTL22 have been shown to play roles in neural, mesenchymal, bone, and hematopoietic stem cell development, respectively. Additionally, a variety of other METTL family members are translational regulators, a role that could place them as important players in the transition from stem cell quiescence to differentiation. Here we will summarize what is known about the role of METTL proteins in stem cell differentiation and highlight the connection between their growing importance in development and their established roles in oncogenesis.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - James P Catlin
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA.
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Wang S, Li H, Liu J, Zhang Q, Xu W, Xiang J, Fang L, Xu P, Li Z. Integrative analysis of m3C associated genes reveals METTL2A as a potential oncogene in breast Cancer. J Transl Med 2022; 20:476. [PMID: 36266694 PMCID: PMC9583565 DOI: 10.1186/s12967-022-03683-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022] Open
Abstract
RNA methylation modifications, especially m6A mRNA modification, are known to be extensively involved in tumor development. However, the relationship between N3-methylcytidine (m3C) related genes and tumorigenesis has rarely been studied. In this research, we found that m3C-related genes were expressed at different levels and affected patients’ prognosis across multiple cancer types from The Cancer Genome Atlas and multi-omics levels. Importantly, methyltransferase-like proteins 2A (METTL2A) had a high amplification frequency (~ 7%) in patients with breast invasive carcinoma (BRCA), and its overexpression was an independent predictor of poor overall survival. Enrichment analysis of associated genes revealed that METTL2A may activate DNA synthesis and cell proliferation pathways in BRCA cells. Through drug sensitivity analysis, Trifluridine, PD407824, and Taselisib were shown to be effective drugs for METTL2A-positive BRCA patients. Overall, our research conducts a holistic view of the expression level and prognostic signature of m3C-related genes with multiple malignancies. Importantly, METTL2A has been intensely explored as a potential oncogene in BRCA, to aid the development of potential drug agents for precision therapy in breast cancer patients.
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Affiliation(s)
- Shuai Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Huiting Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jiheng Liu
- Department of Hematology and Oncology, First Hospital of Changsha, Changsha, Hunan, China
| | - Qianqian Zhang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wei Xu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Juanjuan Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Li Fang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Ping Xu
- Departments of Respiratory and Critical Care Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zheng Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
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Moreno S, Ramos Pittol JM, Hartl M, Micura R. Robust synthesis of 2'-azido modified RNA from 2'-amino precursors by diazotransfer reaction. Org Biomol Chem 2022; 20:7845-7850. [PMID: 36172831 DOI: 10.1039/d2ob01560a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Azides are versatile bioorthogonal reporter moieties that are commonly used for site-specific labeling and functionalization of RNA to probe its biology. The preparation of azido modified nucleic acids by solid-phase synthesis is problematic due to the inherent reactivity of P(III) species with azides according to the Staudinger reaction. Various strategies have been developed to bypass this limitation and are often time-consuming, low-yielding and labor-intensive. In particular, the synthesis of RNA with internal 2'-azido modifications is restricted to a single approach that employs P(V) chemistry instead of the widely used P(III) phosphoramidite chemistry. To fill this methodological gap, we present a novel convenient path toward 2'-azido RNA from readily accessible 2'-amino RNA through treatment with the diazotizing reagent fluorosulfuryl azide (FSO2N3). A diazotransfer reaction was established for oligoribonucleotides of different lengths and secondary structures. The robustness of the approach was further demonstrated for RNAs containing multiple 2'-azido moieties and for RNAs containing other sensitive modifications such as thiouridine or methylated nucleobases with a positive charge. The synthetic ease of generating 2'-azido RNA will pave the way for biotechnological applications, in particular for siRNA technologies and for referencing the growing number of RNA metabolic labeling approaches that rely on 2'-azido nucleosides.
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Affiliation(s)
- Sarah Moreno
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
| | - José M Ramos Pittol
- Institute of Biochemistry, Center for Chemistry and Biomedicine (CCB) Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Markus Hartl
- Institute of Biochemistry, Center for Chemistry and Biomedicine (CCB) Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
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You XJ, Zhang S, Chen JJ, Tang F, He J, Wang J, Qi CB, Feng YQ, Yuan BF. Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA. Nucleic Acids Res 2022; 50:9858-9872. [PMID: 36095124 PMCID: PMC9508817 DOI: 10.1093/nar/gkac770] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/17/2022] [Accepted: 08/27/2022] [Indexed: 11/21/2022] Open
Abstract
RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m6A and m1A), dual methylation modification occurring in the nucleobase of adenosine, such as N6,N6-dimethyladenosine (m6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N6-dimethyladenosine (m1,6A), in tRNAs of living organisms. We confirmed that m1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m1,6A in tRNAs and m1,6A could be demethylated by ALKBH3. Collectively, the discovery of m1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.
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Affiliation(s)
- Xue-Jiao You
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Shan Zhang
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Juan-Juan Chen
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Feng Tang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jingang He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chu-Bo Qi
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Yu-Qi Feng
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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40
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Feng Q, Wang D, Xue T, Lin C, Gao Y, Sun L, Jin Y, Liu D. The role of RNA modification in hepatocellular carcinoma. Front Pharmacol 2022; 13:984453. [PMID: 36120301 PMCID: PMC9479111 DOI: 10.3389/fphar.2022.984453] [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: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Tianyi Xue
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Chao Lin
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Yongjian Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liqun Sun
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Dianfeng Liu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Dianfeng Liu,
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41
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Yang C, Dong Z, Ling Z, Chen Y. The crucial mechanism and therapeutic implication of RNA methylation in bone pathophysiology. Ageing Res Rev 2022; 79:101641. [PMID: 35569786 DOI: 10.1016/j.arr.2022.101641] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Methylation is the most common posttranscriptional modification in cellular RNAs, which has been reported to modulate the alteration of RNA structure for initiating relevant functions such as nuclear translocation and RNA degradation. Recent studies found that RNA methylation especially N6-methyladenosine (m6A) regulates the dynamic balance of bone matrix and forms a complicated network in bone metabolism. The modulation disorder of RNA methylation contributes to several pathological bone diseases including osteoporosis (OP), osteoarthritis (OA), rheumatoid arthritis (RA), and so on. In the review, we will discuss advanced technologies for detecting RNA methylation, summarize RNA methylation-related biological impacts on regulating bone homeostasis and pathological bone diseases. In addition, we focus on the promising roles of RNA methylation in early diagnosis and therapeutic implications for bone-related diseases. Then, we aim to establish a theoretical basis for further investigation in this meaningful field.
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42
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Watkins CP, Zhang W, Wylder AC, Katanski CD, Pan T. A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation. Nat Commun 2022; 13:2491. [PMID: 35513407 PMCID: PMC9072684 DOI: 10.1038/s41467-022-30261-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 12/31/2022] Open
Abstract
Small RNAs include tRNA, snRNA, micro-RNA, tRNA fragments and others that constitute > 90% of RNA copy numbers in a human cell and perform many essential functions. Popular small RNA-seq strategies limit the insights into coordinated small RNA response to cellular stress. Small RNA-seq also lacks multiplexing capabilities. Here, we report a multiplex small RNA-seq library preparation method (MSR-seq) to investigate cellular small RNA and mRNA response to heat shock, hydrogen peroxide, and arsenite stress. Comparing stress-induced changes of total cellular RNA and polysome-associated RNA, we identify a coordinated tRNA response that involves polysome-specific tRNA abundance and synergistic N3-methylcytosine (m3C) tRNA modification. Combining tRNA and mRNA response to stress we reveal a mechanism of stress-induced down-regulation in translational elongation. We also find that native tRNA molecules lacking several modifications are biased reservoirs for the biogenesis of tRNA fragments. Our results demonstrate the importance of simultaneous investigation of small RNAs and their modifications in response to varying biological conditions.
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Affiliation(s)
- Christopher P. Watkins
- grid.170205.10000 0004 1936 7822Department of Biochemistry and Molecular Biology, Chicago, IL 60637 USA
| | - Wen Zhang
- grid.170205.10000 0004 1936 7822Department of Chemistry, University of Chicago, Chicago, IL 60637 USA
| | - Adam C. Wylder
- grid.170205.10000 0004 1936 7822Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637 USA
| | - Christopher D. Katanski
- grid.170205.10000 0004 1936 7822Department of Biochemistry and Molecular Biology, Chicago, IL 60637 USA
| | - Tao Pan
- grid.170205.10000 0004 1936 7822Department of Biochemistry and Molecular Biology, Chicago, IL 60637 USA
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43
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Role of main RNA modifications in cancer: N 6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct Target Ther 2022; 7:142. [PMID: 35484099 PMCID: PMC9051163 DOI: 10.1038/s41392-022-01003-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied several common RNA modifications, such as N6-methyladenosine, 5-methylcytosine, and pseudouridine. The deposition and roles of these modifications in coding and noncoding RNAs are summarized in detail. Based on the RNA modification background, this review summarized the expression, function, and underlying molecular mechanism of these modifications and their regulators in cancer and further discussed the role of some existing small-molecule inhibitors. More in-depth studies on RNA modification and cancer are needed to broaden the understanding of epigenetics and cancer diagnosis, treatment, and prognosis.
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44
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Xu L, Peng B, Wu H, Zheng Y, Yu Q, Fang S. METTL7B contributes to the malignant progression of glioblastoma by inhibiting EGR1 expression. Metab Brain Dis 2022; 37:1133-1143. [PMID: 35254598 DOI: 10.1007/s11011-022-00925-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/31/2022] [Indexed: 11/26/2022]
Abstract
Glioblastoma (GBM), a predominant central nervous system (CNS) malignancy, is correlated with high mortality and severe morbidity. Mammalian methyltransferase-like 7B (METTL7B) as a methyltransferase has been identified to participate in cancer progression. However, its function in GBM is elusive. Accordingly, we aimed to explore the effect of METTL7B on GBM. The expression of METTL7B and EGR2 in GBM patients and GBM cells were detected by qPCR, western blots and immunohistochemical staining. Cell viability was assessed by CCK-8 assays. Cell proliferation was determined by EdU, colony formation, and tumor sphere formation assays. METTL7B shRNA was injected into the Balb/c nude mice. The size and weight of isolated tumor was measured. And the expression levels of Ki67, METTL7B and EGR1 were examined by immunohistochemical staining. METTL7B was significantly elevated, while EGR1 was downregulated in clinical GBM tissues. METTL7B upregulation was associated with the low overall survival of GBM patients. Moreover, METTL7B depletion remarkably attenuated GBM cell proliferation. Mechanistically, METTL7B overexpression inhibited EGR1 expression in GBM cells. EGR1 knockdown rescued the inhibitory effect of METTL7B depletion on GBM cell proliferation. Meanwhile, METTL7B depletion arrested more GBM cells at the G0/G1, but fewer cells at the S phase, which EGR1 knockdown reversed these effects. Furthermore, tumorigenicity analysis revealed that METTL7B promotes tumor growth of GBM cells in vivo. METTL7B contributes to the malignant progression of GBM by inhibiting EGR1 expression. METTL7B and EGR1 may be utilized as the treatment targets for GBM therapy.
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Affiliation(s)
- Li Xu
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China.
| | - Biao Peng
- Deparment of Neurosurgery, the Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou City, Guangdong Province, 510080, People's Republic of China
| | - Haiqiang Wu
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
| | - Yike Zheng
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
| | - Qingwen Yu
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
| | - Shuiqiao Fang
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
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45
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Biological roles of RNA m 5C modification and its implications in Cancer immunotherapy. Biomark Res 2022; 10:15. [PMID: 35365216 PMCID: PMC8973801 DOI: 10.1186/s40364-022-00362-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetics including DNA and RNA modifications have always been the hotspot field of life sciences in the post-genome era. Since the first mapping of N6-methyladenosine (m6A) and the discovery of its widespread presence in mRNA, there are at least 160-170 RNA modifications have been discovered. These methylations occur in different RNA types, and their distribution is species-specific. 5-methylcytosine (m5C) has been found in mRNA, rRNA and tRNA of representative organisms from all kinds of species. As reversible epigenetic modifications, m5C modifications of RNA affect the fate of the modified RNA molecules and play important roles in various biological processes including RNA stability control, protein synthesis, and transcriptional regulation. Furthermore, accumulative evidence also implicates the role of RNA m5C in tumorigenesis. Here, we review the latest progresses in the biological roles of m5C modifications and how it is regulated by corresponding “writers”, “readers” and “erasers” proteins, as well as the potential molecular mechanism in tumorigenesis and cancer immunotherapy.
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46
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Zhang W, Foo M, Eren AM, Pan T. tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Mol Cell 2022; 82:891-906. [PMID: 35032425 PMCID: PMC8897278 DOI: 10.1016/j.molcel.2021.12.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/17/2022]
Abstract
tRNA is the most extensively modified RNA in cells. On average, a bacterial tRNA contains 8 modifications per molecule and a eukaryotic tRNA contains 13 modifications per molecule. Recent studies reveal that tRNA modifications are highly dynamic and respond extensively to environmental conditions. Functions of tRNA modification dynamics include enhanced, on-demand decoding of specific codons in response genes and regulation of tRNA fragment biogenesis. This review summarizes recent advances in the studies of tRNA modification dynamics in biological processes, tRNA modification erasers, and human-associated bacteria. Furthermore, we use the term "metaepitranscriptomics" to describe the potential and approach of tRNA modification studies in natural biological communities such as microbiomes. tRNA is highly modified in cells, and tRNA modifications respond extensively to environmental conditions to enhance translation of specific genes and produce tRNA fragments on demand. We review recent advances in tRNA sequencing methods, tRNA modification dynamics in biological processes, and tRNA modification studies in natural communities such as the microbiomes.
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Affiliation(s)
- Wen Zhang
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Marcus Foo
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - A. Murat Eren
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA;,Department of Medicine, University of Chicago, Chicago, IL 60637, USA;,Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
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47
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Lentini JM, Bargabos R, Chen C, Fu D. Methyltransferase METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs. J Biol Chem 2022; 298:101788. [PMID: 35247384 PMCID: PMC8980813 DOI: 10.1016/j.jbc.2022.101788] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/03/2023] Open
Abstract
A subset of eukaryotic tRNAs is methylated in the anticodon loop, forming 3-methylcytosine (m3C) modifications. In mammals, the number of tRNAs containing m3C modifications has been expanded to include mitochondrial (mt) tRNA-Ser-UGA and mt-tRNA-Thr-UGU. However, whereas the enzymes catalyzing m3C formation in nuclear-encoded tRNAs have been identified, the proteins responsible for m3C modification in mt-tRNAs are unknown. Here, we show that m3C formation in human mt-tRNAs is dependent upon the Methyltransferase-Like 8 (METTL8) enzyme. We find that METTL8 is a mitochondria-associated protein that interacts with mitochondrial seryl-tRNA synthetase, as well as with mt-tRNAs containing m3C. We demonstrate that human cells deficient in METTL8 exhibit loss of m3C modification in mt-tRNAs, but not nuclear-encoded tRNAs. Consistent with the mitochondrial import of METTL8, the formation of m3C in METTL8-deficient cells could be rescued by re-expression of wildtype METTL8, but not by a METTL8 variant lacking the N-terminal mitochondrial localization signal. Notably, we found METTL8-deficiency in human cells causes alterations in the native migration pattern of mt-tRNA-Ser-UGA, suggesting a role for m3C in tRNA folding. Altogether, these findings demonstrate that METTL8 is required for m3C formation in mitochondrial tRNAs and uncover a potential function for m3C modification in mitochondrial tRNA structure.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Rachel Bargabos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Chen Chen
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America.
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48
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Bohnsack KE, Kleiber N, Lemus-Diaz N, Bohnsack MT. Roles and dynamics of 3-methylcytidine in cellular RNAs. Trends Biochem Sci 2022; 47:596-608. [DOI: 10.1016/j.tibs.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 01/02/2023]
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49
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Evke S, Lin Q, Melendez JA, Begley TJ. Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen. Genes (Basel) 2022; 13:genes13030421. [PMID: 35327975 PMCID: PMC8955276 DOI: 10.3390/genes13030421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how acute toxic doses of pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNASec) to translationally regulate the production of glutathione peroxidases (Gpx’s) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of many RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm5U), isopentenyladenosine (i6A), pseudouridine (Ψ), and 1-methyladenosine (m1A) modifications linked to tRNASec and many other tRNA’s. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.
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Affiliation(s)
- Sara Evke
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Qishan Lin
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Juan Andres Melendez
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Thomas John Begley
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
- Correspondence:
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50
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Synthesis of N4-acetylated 3-methylcytidine phosphoramidites for RNA solid-phase synthesis. MONATSHEFTE FUR CHEMIE 2022; 153:285-291. [PMID: 35400759 PMCID: PMC8948120 DOI: 10.1007/s00706-022-02896-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/31/2022] [Indexed: 01/10/2023]
Abstract
The growing interest in 3-methylcytidine (m3C) originates from the recent discoveries of m3C modified tRNAs in humans as well as its intensively debated occurrence in mRNA. Moreover, m3C formation can be catalyzed by RNA without the assistance of proteins as has been demonstrated for a naturally occurring riboswitch fold using the methylated form of its cognate ligand as cofactor. Additionally, new RNA sequencing methods have been developed to detect this modification in transcriptome-wide manner. For all these reasons, an increasing demand for synthetic m3C containing oligoribonucleotides is emerging. Their chemical synthesis relies on RNA solid-phase synthesis using phosphoramidite building blocks. Here, we describe a facile synthetic path towards N4-acetylated 2′-O-TBDMS- and 2′-O-TOM m3C phosphoramidites to provide an optimal toolbox for solid-phase synthesis of m3C containing RNA.
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