301
|
Li C, Peng D, Gan Y, Zhou L, Hou W, Wang B, Yuan P, Xiong W, Wang L. The m 6A methylation landscape, molecular characterization and clinical relevance in prostate adenocarcinoma. Front Immunol 2023; 14:1086907. [PMID: 37033963 PMCID: PMC10076583 DOI: 10.3389/fimmu.2023.1086907] [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: 11/01/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Background Despite the recent progress of therapeutic strategies in treating prostate cancer (PCa), the majority of patients still eventually relapse, experiencing dismal outcomes. Therefore, it is of utmost importance to identify novel viable targets to increase the effectiveness of treatment. The present study aimed to investigate the potential relationship between N6-methyladenosine (m6A) RNA modification and PCa development and determine its clinical relevance. Methods Through systematic analysis of the TCGA database and other datasets, we analyzed the gene expression correlation and mutation profiles of m6A-related genes between PCa and normal tissues. Patient samples were divided into high- and low-risk groups based on the results of Least Absolute Shrinkage and Selection Operator (LASSO) Cox analysis. Subsequently, differences in biological processes and genomic characteristics of the two risk groups were determined, followed by functional enrichment analysis and gene set enrichment (GSEA) analysis. Next, we constructed the protein-protein interaction (PPI) network of differentially expressed genes between patients in high- and low-risk groups, along with the mRNA-miRNA-lncRNA network. The correlation analysis of tumor-infiltrating immune cells was further conducted to reveal the differences in immune characteristics between the two groups. Results A variety of m6A-related genes were identified to be differentially expressed in PCa tissues as compared with normal tissues. In addition, the PPI network contained 278 interaction relationships and 34 m6A-related genes, and the mRNA-miRNA-lncRNA network contained 17 relationships, including 91 miRNAs. Finally, the immune characteristics analysis showed that compared with the low-risk group, the levels of M1 and M2 macrophages in the high-risk group significantly increased, while the levels of mast cells resting and T cells CD4 memory resting significantly decreased. Conclusions This study provides novel findings that can further the understanding of the role of m6A methylation during the progression of PCa, which may facilitate the invention of targeted therapeutic drugs.
Collapse
Affiliation(s)
- Chao Li
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Dongyi Peng
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yu Gan
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Lei Zhou
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Weibin Hou
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Bingzhi Wang
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Peng Yuan
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Wei Xiong
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Long Wang
- Department of Urology, Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Long Wang,
| |
Collapse
|
302
|
Martinez De La Cruz B, Darsinou M, Riccio A. From form to function: m 6A methylation links mRNA structure to metabolism. Adv Biol Regul 2023; 87:100926. [PMID: 36513580 PMCID: PMC10585597 DOI: 10.1016/j.jbior.2022.100926] [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: 09/23/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Reversible N6-methyladenosine (m6A) RNA modification is a posttranscriptional epigenetic modification of the RNA that regulates many key aspects of RNA metabolism and function. In this review, we highlight major recent advances in the field, with special emphasis on the potential link between m6A modifications and RNA structure. We will also discuss the role of RNA methylation of neuronal transcripts, and the emerging evidence of a potential role in RNA transport and local translation in dendrites and axons of transcripts involved in synaptic functions and axon growth.
Collapse
Affiliation(s)
| | - Marousa Darsinou
- UCL Laboratory for Molecular Cell Biology - University College London, Gower Street, WC1E 6BT, London, UK
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology - University College London, Gower Street, WC1E 6BT, London, UK.
| |
Collapse
|
303
|
Ding JH, Chen MY, Xie NB, Xie C, Xiong N, He JG, Wang J, Guo C, Feng YQ, Yuan BF. Quantitative and site-specific detection of inosine modification in RNA by acrylonitrile labeling-mediated elongation stalling. Biosens Bioelectron 2023; 219:114821. [PMID: 36279821 DOI: 10.1016/j.bios.2022.114821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/04/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022]
Abstract
RNA molecules contain diverse modifications that play crucial roles in a wide variety of biological processes. Inosine is one of the most prevalent modifications in RNA and dysregulation of inosine is correlated with many human diseases. Herein, we established an acrylonitrile labeling-mediated elongation stalling (ALES) method for quantitative and site-specific detection of inosine in RNA from biological samples. In ALES method, inosine is selectively cyanoethylated with acrylonitrile to form N1-cyanoethylinosine (ce1I) through a Michael addition reaction. The N1-cyanoethyl group of ce1I compromises the hydrogen bond between ce1I and other nucleobases, leading to the stalling of reverse transcription at original inosine site. This specific property of stalling at inosine site could be evaluated by subsequent real-time quantitative PCR (qPCR). With the proposed ALES method, we found the significantly increased level of inosine at position Chr1:63117284 of Ino80dos RNA of multiple tissues from sleep-deprived mice compared to the control mice. This is the first report on the investigation of inosine modification in sleep-deprived mice, which may open up new direction for deciphering insomnia from RNA modifications. In addition, we found the decreased level of inosine at GluA2 Q/R site (Chr4:157336723) in glioma tissues, indicating the decreased level of inosine at GluA2 Q/R site may serve as potential indicator for the diagnosis of glioma. Taken together, the proposed ALES method is capable of quantitative and site-specific detection of inosine in RNA, which provides a valuable tool to uncover the functions of inosine in human diseases.
Collapse
Affiliation(s)
- Jiang-Hui Ding
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Meng-Yuan Chen
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Neng-Bin Xie
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| | - Conghua Xie
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| | - Nanxiang Xiong
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| | - Jin-Gang 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, 430071, Wuhan, 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, 430071, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yu-Qi Feng
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Bi-Feng Yuan
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China.
| |
Collapse
|
304
|
Jürgenstein K, Tagel M, Ilves H, Leppik M, Kivisaar M, Remme J. Variance in translational fidelity of different bacterial species is affected by pseudouridines in the tRNA anticodon stem-loop. RNA Biol 2022; 19:1050-1058. [PMID: 36093925 PMCID: PMC9481147 DOI: 10.1080/15476286.2022.2121447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Delicate variances in the translational machinery affect how efficiently different organisms approach protein synthesis. Determining the scale of this effect, however, requires knowledge on the differences of mistranslation levels. Here, we used a dual-luciferase reporter assay cloned into a broad host range plasmid to reveal the translational fidelity profiles of Pseudomonas putida, Pseudomonas aeruginosa and Escherichia coli. We observed that these profiles are surprisingly different, whereas species more prone to translational frameshifting are not necessarily more prone to stop codon readthrough. As tRNA modifications are among the factors that have been implicated to affect translation accuracy, we also show that translational fidelity is context-specifically influenced by pseudouridines in the anticodon stem-loop of tRNA, but the effect is not uniform between species.
Collapse
Affiliation(s)
- Karl Jürgenstein
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mari Tagel
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Heili Ilves
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Margus Leppik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| |
Collapse
|
305
|
Wang X, Guo Z, Yan F. RNA Epigenetics in Chronic Lung Diseases. Genes (Basel) 2022; 13:genes13122381. [PMID: 36553648 PMCID: PMC9777603 DOI: 10.3390/genes13122381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including N6 methylation of adenosine (m6A), N1 methylation of adenosine (m1A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), 2'O-methylation (2'-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.
Collapse
Affiliation(s)
- Xiaorui Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Zhihou Guo
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Furong Yan
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
- Correspondence:
| |
Collapse
|
306
|
The role of post-transcriptional modifications during development. Biol Futur 2022:10.1007/s42977-022-00142-3. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
Collapse
|
307
|
Chen C, Ye L. The m1A modification of tRNAs: a translational accelerator of T-cell activation. Cell Mol Immunol 2022; 19:1328-1329. [PMID: 36336727 PMCID: PMC9709032 DOI: 10.1038/s41423-022-00942-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Cheng Chen
- Institute of Immunology, Third Military Medical University, Chongqing, 400038, China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, 400038, China.
| |
Collapse
|
308
|
Prokhorova DV, Vokhtantsev IP, Tolstova PO, Zhuravlev ES, Kulishova LM, Zharkov DO, Stepanov GA. Natural Nucleoside Modifications in Guide RNAs Can Modulate the Activity of the CRISPR-Cas9 System In Vitro. CRISPR J 2022; 5:799-812. [PMID: 36350691 DOI: 10.1089/crispr.2022.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
At the present time, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has been widely adopted as an efficient genomic editing tool. However, there are some actual problems such as the off-target effects, cytotoxicity, and immunogenicity. The incorporation of modifications into guide RNAs permits enhancing both the efficiency and the specificity of the CRISPR-Cas9 system. In this study, we demonstrate that the inclusion of N6-methyladenosine, 5-methylcytidine, and pseudouridine in trans-activating RNA (tracrRNA) or in single guide RNA (sgRNA) enables efficient gene editing in vitro. We found that the complexes of modified guide RNAs with Cas9 protein promoted cleavage of the target short/long duplexes and plasmid substrates. In addition, the modified monomers in guide RNAs allow increasing the specificity of CRISPR-Cas9 system in vitro and promote diminishing both the immunostimulating and the cytotoxic effects of sgRNAs.
Collapse
Affiliation(s)
- Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ivan P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina O Tolstova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lilia M Kulishova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
309
|
Lee MY, Ojeda-Britez S, Ehrbar D, Samwer A, Begley TJ, Melendez JA. Selenoproteins and the senescence-associated epitranscriptome. Exp Biol Med (Maywood) 2022; 247:2090-2102. [PMID: 36036467 PMCID: PMC9837304 DOI: 10.1177/15353702221116592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Selenium is a naturally found trace element, which provides multiple benefits including antioxidant, anticancer, and antiaging, as well as boosting immunity. One unique feature of selenium is its incorporation as selenocysteine, a rare 21st amino acid, into selenoproteins. Twenty-five human selenoproteins have been discovered, and a majority of these serve as crucial antioxidant enzymes for redox homeostasis. Unlike other amino acids, incorporation of selenocysteine requires a distinctive UGA stop codon recoding mechanism. Although many studies correlating selenium, selenoproteins, aging, and senescence have been performed, it has not yet been explored if the upstream events regulating selenoprotein synthesis play a role in senescence-associated pathologies. The epitranscriptomic writer alkylation repair homolog 8 (ALKBH8) is critical for selenoprotein production, and its deficiency can significantly decrease levels of selenoproteins that are essential for reactive oxygen species (ROS) detoxification, and increase oxidative stress, one of the major drivers of cellular senescence. Here, we review the potential role of epitranscriptomic marks that govern selenocysteine utilization in regulating the senescence program.
Collapse
Affiliation(s)
- May Y Lee
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
- The RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Stephen Ojeda-Britez
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Dylan Ehrbar
- 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
| | | | - Thomas J 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
| | - J Andres Melendez
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
- The RNA Institute, University at Albany, Albany, NY 12222, USA
| |
Collapse
|
310
|
Hong J, Xu K, Lee JH. Biological roles of the RNA m 6A modification and its implications in cancer. Exp Mol Med 2022; 54:1822-1832. [PMID: 36446846 PMCID: PMC9722703 DOI: 10.1038/s12276-022-00897-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/30/2022] Open
Abstract
The N6-Methyladenosine (m6A) modification of RNA transcripts is the most prevalent and abundant internal modification in eukaryotic messenger RNAs (mRNAs) and plays diverse and important roles in normal biological processes. Extensive studies have indicated that dysregulated m6A modification and m6A-associated proteins play critical roles in tumorigenesis and cancer progression. However, m6A-mediated physiological consequences often lead to opposite outcomes in a biological context-dependent manner. Therefore, context-related complexity must be meaningfully considered to obtain a comprehensive understanding of RNA methylation. Recently, it has been reported that m6A-modified RNAs are closely related to the regulation of the DNA damage response and genomic integrity maintenance. Here, we present an overview of the current knowledge on the m6A modification and its function in human cancer, particularly in relation to the DNA damage response and genomic instability.
Collapse
Affiliation(s)
- Juyeong Hong
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Kexin Xu
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Ji Hoon Lee
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| |
Collapse
|
311
|
Lombard M, Reed CJ, Pecqueur L, Faivre B, Toubdji S, Sudol C, Brégeon D, de Crécy-Lagard V, Hamdane D. Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family. Biomolecules 2022; 12:1760. [PMID: 36551188 PMCID: PMC9775027 DOI: 10.3390/biom12121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Dihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus). So far, only bacterial Dus enzymes and their complexes with tRNAs have been structurally characterized. Understanding the structure-function relationships of eukaryotic Dus proteins has been hampered by the paucity of structural data. Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. Dus2 is the eukaryotic enzyme responsible for the synthesis of D20 in tRNAs and is involved in some human cancers and in the detoxification of β-amyloid peptides in Alzheimer's disease. In addition to the domains forming the canonical structure of all Dus, i.e., the catalytic TIM-barrel domain and the helical domain, both participating in RNA recognition in the bacterial Dus, a majority of Dus2 proteins harbor extensions at both ends. While these are mainly unstructured extensions on the N-terminal side, the C-terminal side extensions can adopt well-defined structures such as helices and beta-sheets or even form additional domains such as zinc finger domains. 3D models of Dus2/tRNA complexes were also generated. This study suggests that eukaryotic Dus2 proteins may have an advantage in tRNA recognition over their bacterial counterparts due to their modularity.
Collapse
Affiliation(s)
- Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Sabrine Toubdji
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
- IBPS, Biology of Aging and Adaptation, Sorbonne Université 7 quai Saint Bernard, CEDEX 05, 75252 Paris, France
| | - Claudia Sudol
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
- IBPS, Biology of Aging and Adaptation, Sorbonne Université 7 quai Saint Bernard, CEDEX 05, 75252 Paris, France
| | - Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne Université 7 quai Saint Bernard, CEDEX 05, 75252 Paris, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Université Pierre et Marie Curie, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| |
Collapse
|
312
|
Yang Z, Zhang S, Xia T, Fan Y, Shan Y, Zhang K, Xiong J, Gu M, You B. RNA Modifications Meet Tumors. Cancer Manag Res 2022; 14:3223-3243. [PMID: 36444355 PMCID: PMC9700476 DOI: 10.2147/cmar.s391067] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/11/2022] [Indexed: 09/14/2023] Open
Abstract
RNA modifications occur through the whole process of gene expression regulation, including transcription, translation, and post-translational processes. They are closely associated with gene expression, RNA stability, and cell cycle. RNA modifications in tumor cells play a vital role in tumor development and metastasis, changes in the tumor microenvironment, drug resistance in tumors, construction of tumor cell-cell "internet", etc. Several types of RNA modifications have been identified to date and have various effects on the biological characteristics of different tumors. In this review, we discussed the function of RNA modifications, including N 6-methyladenine (m6A), 5-methylcytosine (m5C), N 7-methyladenosine (m7G), N 1-methyladenosine (m1A), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I), in the microenvironment and therapy of solid and liquid tumors.
Collapse
Affiliation(s)
- Zhiyuan Yang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Siyu Zhang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Tian Xia
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Yue Fan
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Ying Shan
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Kaiwen Zhang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Jiayan Xiong
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Miao Gu
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| | - Bo You
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, People’s Republic of China
| |
Collapse
|
313
|
Lei HT, Wang ZH, Li B, Sun Y, Mei SQ, Yang JH, Qu LH, Zheng LL. tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data. Nucleic Acids Res 2022; 51:D315-D327. [PMID: 36408909 PMCID: PMC9825477 DOI: 10.1093/nar/gkac1087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
tRNA molecules contain dense, abundant modifications that affect tRNA structure, stability, mRNA decoding and tsRNA formation. tRNA modifications and related enzymes are responsive to environmental cues and are associated with a range of physiological and pathological processes. However, there is a lack of resources that can be used to mine and analyse these dynamically changing tRNA modifications. In this study, we established tModBase (https://www.tmodbase.com/) for deciphering the landscape of tRNA modification profiles from epitranscriptome data. We analysed 103 datasets generated with second- and third-generation sequencing technologies and illustrated the misincorporation and termination signals of tRNA modification sites in ten species. We thus systematically demonstrate the modification profiles across different tissues/cell lines and summarize the characteristics of tRNA-associated human diseases. By integrating transcriptome data from 32 cancers, we developed novel tools for analysing the relationships between tRNA modifications and RNA modification enzymes, the expression of 1442 tRNA-derived small RNAs (tsRNAs), and 654 DNA variations. Our database will provide new insights into the features of tRNA modifications and the biological pathways in which they participate.
Collapse
Affiliation(s)
- Hao-Tian Lei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Zhang-Hao Wang
- Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yang Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Shi-Qiang Mei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jian-Hua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Liang-Hu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Ling-Ling Zheng
- To whom correspondence should be addressed. Tel: +86 20 84112399; Fax: +86 20 84036551;
| |
Collapse
|
314
|
Zhang X, Yin H, Zhang X, Jiang X, Liu Y, Zhang H, Peng Y, Li D, Yu Y, Zhang J, Cheng S, Yang A, Zhang R. N6-methyladenosine modification governs liver glycogenesis by stabilizing the glycogen synthase 2 mRNA. Nat Commun 2022; 13:7038. [PMID: 36396934 PMCID: PMC9671881 DOI: 10.1038/s41467-022-34808-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatic glycogen is the main source of blood glucose and controls the intervals between meals in mammals. Hepatic glycogen storage in mammalian pups is insufficient compared to their adult counterparts; however, the detailed molecular mechanism is poorly understood. Here, we show that, similar to glycogen storage pattern, N6-methyladenosine (m6A) modification in mRNAs gradually increases during the growth of mice in liver. Strikingly, in the hepatocyte-specific Mettl3 knockout mice, loss of m6A modification disrupts liver glycogen storage. On the mechanism, mRNA of Gys2, the liver-specific glycogen synthase, is a substrate of METTL3 and plays a critical role in m6A-mediated glycogenesis. Furthermore, IGF2BP2, a "reader" protein of m6A, stabilizes the mRNA of Gys2. More importantly, reconstitution of GYS2 almost rescues liver glycogenesis in Mettl3-cKO mice. Collectively, a METTL3-IGF2BP2-GYS2 axis, in which METTL3 and IGF2BP2 regulate glycogenesis as "writer" and "reader" proteins respectively, is essential on maintenance of liver glycogenesis in mammals.
Collapse
Affiliation(s)
- Xiang Zhang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China ,grid.233520.50000 0004 1761 4404The Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Huilong Yin
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China ,grid.412990.70000 0004 1808 322XThe Henan Key Laboratory of immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003 China ,grid.412990.70000 0004 1808 322XThe Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003 China
| | - Xiaofang Zhang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Xunliang Jiang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Yongkang Liu
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Haolin Zhang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Yingran Peng
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Da Li
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Yanping Yu
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China ,grid.440201.30000 0004 1758 2596The Second Ward of Gynecological Tumor, Shaanxi Provincial Tumor Hospital, Xi’an, Shaanxi 710000 China
| | - Jinbao Zhang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Shuli Cheng
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China ,grid.43169.390000 0001 0599 1243The Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Laboratory Center of Stomatology, Department of Orthodontics, College of Stomatology, Xi’an Jiaotong University, Xi’an, Shaanxi 710032 China
| | - Angang Yang
- grid.412990.70000 0004 1808 322XThe Henan Key Laboratory of immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003 China ,grid.412990.70000 0004 1808 322XThe Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003 China ,grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Rui Zhang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China ,grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| |
Collapse
|
315
|
Zhang Y, Jiang J, Ma J, Wei Z, Wang Y, Song B, Meng J, Jia G, de Magalhães JP, Rigden D, Hang D, Chen K. DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. Nucleic Acids Res 2022; 51:D106-D116. [PMID: 36382409 PMCID: PMC9825532 DOI: 10.1093/nar/gkac1061] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antibody immunoprecipitation methods for particular modification types. They also face the problem of short read length, isoform ambiguities, biases and artifacts. Direct RNA sequencing (DRS) technologies, commercialized by Oxford Nanopore Technologies (ONT), enable the direct interrogation of any given modification present in individual transcripts and promise to address the limitations of previous NGS-based methods. Here, we present the first ONT-based database of quantitative RNA modification profiles, DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies. In addition to standard functions adopted by existing databases, such as gene annotations and post-transcriptional association analysis, we provide a fresh view of RNA modifications, which enables exploration of the epitranscriptome in an isoform-specific manner. The DirectRMDB database is freely available at: http://www.rnamd.org/directRMDB/.
Collapse
Affiliation(s)
| | | | | | - Zhen Wei
- Correspondence may also be addressed to Zhen Wei.
| | - Yue Wang
- Department of Mathematical Sciences, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,Department of Computer Science, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Bowen Song
- Department of Mathematical Sciences, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,Institute of Systems, Molecular and Integrative Biology, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Jia Meng
- Department of Biological Sciences, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China,Institute of Systems, Molecular and Integrative Biology, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - João Pedro de Magalhães
- Institute of Life Course and Medical Sciences, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, Xi’anJiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Daiyun Hang
- Correspondence may also be addressed to Daiyun Hang.
| | - Kunqi Chen
- To whom correspondence should be addressed. Tel: +86 0591 22862299;
| |
Collapse
|
316
|
Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
Collapse
Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | | | | | | |
Collapse
|
317
|
Conservation and Diversification of tRNA t6A-Modifying Enzymes across the Three Domains of Life. Int J Mol Sci 2022; 23:ijms232113600. [PMID: 36362385 PMCID: PMC9654439 DOI: 10.3390/ijms232113600] [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: 10/09/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification occurs at position 37 of tRNAs that decipher codons starting with adenosine. Mechanistically, t6A stabilizes structural configurations of the anticodon stem loop, promotes anticodon–codon pairing and safeguards the translational fidelity. The biosynthesis of tRNA t6A is co-catalyzed by two universally conserved protein families of TsaC/Sua5 (COG0009) and TsaD/Kae1/Qri7 (COG0533). Enzymatically, TsaC/Sua5 protein utilizes the substrates of L-threonine, HCO3−/CO2 and ATP to synthesize an intermediate L-threonylcarbamoyladenylate, of which the threonylcarbamoyl-moiety is subsequently transferred onto the A37 of substrate tRNAs by the TsaD–TsaB –TsaE complex in bacteria or by the KEOPS complex in archaea and eukaryotic cytoplasm, whereas Qri7/OSGEPL1 protein functions on its own in mitochondria. Depletion of tRNA t6A interferes with protein homeostasis and gravely affects the life of unicellular organisms and the fitness of higher eukaryotes. Pathogenic mutations of YRDC, OSGEPL1 and KEOPS are implicated in a number of human mitochondrial and neurological diseases, including autosomal recessive Galloway–Mowat syndrome. The molecular mechanisms underscoring both the biosynthesis and cellular roles of tRNA t6A are presently not well elucidated. This review summarizes current mechanistic understandings of the catalysis, regulation and disease implications of tRNA t6A-biosynthetic machineries of three kingdoms of life, with a special focus on delineating the structure–function relationship from perspectives of conservation and diversity.
Collapse
|
318
|
RNADSN: Transfer-Learning 5-Methyluridine (m5U) Modification on mRNAs from Common Features of tRNA. Int J Mol Sci 2022; 23:ijms232113493. [PMID: 36362279 PMCID: PMC9655583 DOI: 10.3390/ijms232113493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
One of the most abundant non-canonical bases widely occurring on various RNA molecules is 5-methyluridine (m5U). Recent studies have revealed its influences on the development of breast cancer, systemic lupus erythematosus, and the regulation of stress responses. The accurate identification of m5U sites is crucial for understanding their biological functions. We propose RNADSN, the first transfer learning deep neural network that learns common features between tRNA m5U and mRNA m5U to enhance the prediction of mRNA m5U. Without seeing the experimentally detected mRNA m5U sites, RNADSN has already outperformed the state-of-the-art method, m5UPred. Using mRNA m5U classification as an additional layer of supervision, our model achieved another distinct improvement and presented an average area under the receiver operating characteristic curve (AUC) of 0.9422 and an average precision (AP) of 0.7855. The robust performance of RNADSN was also verified by cross-technical and cross-cellular validation. The interpretation of RNADSN also revealed the sequence motif of common features. Therefore, RNADSN should be a useful tool for studying m5U modification.
Collapse
|
319
|
Mikawy NN, Roy HA, Israel E, Hamlow LA, Zhu Y, Berden G, Oomens J, Frieler CE, Rodgers MT. 5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2165-2180. [PMID: 36279168 DOI: 10.1021/jasms.2c00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.
Collapse
Affiliation(s)
- Neven N Mikawy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - G Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - C E Frieler
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| |
Collapse
|
320
|
Abstract
The field of epitranscriptomics has expanded dramatically in recent years, both in the number of identified RNA modifications and the number of researchers studying them. As knowledge of post-transcriptional modifications continues to expand, numerous new methods have been developed to detect these modifications. Additionally, modifications are being extended to therapeutic settings, such as with recent mRNA vaccines. With this increase in knowledge and use, the community is recognizing the necessity for user-friendly databases to (i) store information from both high- and low-throughput studies and (ii) provide prediction software on how RNA modifications contribute to RNA function and disease. This mini-review highlights select RNA modification databases and their key attributes with the aim of providing a resource to researchers in the field of epitranscriptomics.
Collapse
Affiliation(s)
- Jillian Ramos
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, Colorado 80045, USA
| |
Collapse
|
321
|
Zhang J, Xu C. Gene product diversity: adaptive or not? Trends Genet 2022; 38:1112-1122. [PMID: 35641344 PMCID: PMC9560964 DOI: 10.1016/j.tig.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 01/24/2023]
Abstract
One gene does not equal one RNA or protein. The genomic revolution has revealed numerous different RNA and protein molecules that can be produced from one gene, such as circular RNAs generated by back-splicing, proteins with residues mismatching the genomic encoding because of RNA editing, and proteins extended in the C terminus via stop codon readthrough in translation. Are these diverse products results of exquisite gene regulations or imprecise biological processes? While there are cases where the gene product diversity appears beneficial, genome-scale patterns suggest that much of this diversity arises from nonadaptive, molecular errors. This finding has important implications for studying the functions of diverse gene products and for understanding the fundamental properties and evolution of cellular life.
Collapse
Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Chuan Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
322
|
Dysfunctional tRNA reprogramming and codon-biased translation in cancer. Trends Mol Med 2022; 28:964-978. [PMID: 36241532 PMCID: PMC10071289 DOI: 10.1016/j.molmed.2022.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/20/2022] [Accepted: 09/12/2022] [Indexed: 12/17/2022]
Abstract
Many cancers hijack translation to increase the synthesis of tumor-driving proteins, the messenger mRNAs of which have specific codon usage patterns. Termed 'codon-biased translation' and originally identified in stress response regulation, this mechanism is supported by diverse studies demonstrating how the 50 RNA modifications of the epitranscriptome, specific tRNAs, and codon-biased mRNAs are used by oncogenic programs to promote proliferation and chemoresistance. The epitranscriptome writers METTL1-WDR4, Elongator complex protein (ELP)1-6, CTU1-2, and ALKBH8-TRM112 illustrate the principal mechanism of codon-biased translation, with gene amplifications, increased RNA modifications, and enhanced tRNA stability promoting cancer proliferation. Furthermore, systems-level analyses of 34 tRNA writers and 493 tRNA genes highlight the theme of tRNA epitranscriptome dysregulation in many cancers and identify candidate tRNA writers, tRNA modifications, and tRNA molecules as drivers of pathological codon-biased translation.
Collapse
|
323
|
Begik O, Mattick JS, Novoa EM. Exploring the epitranscriptome by native RNA sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1430-1439. [PMID: 36104106 PMCID: PMC9745831 DOI: 10.1261/rna.079404.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
Collapse
Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra, Barcelona 08002, Spain
| |
Collapse
|
324
|
Katanski CD, Alshammary H, Watkins CP, Huang S, Gonzales-Reiche A, Sordillo EM, van Bakel H, Lolans K, Simon V, Pan T. tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity. Front Cell Dev Biol 2022; 10:999351. [PMID: 36393870 PMCID: PMC9664364 DOI: 10.3389/fcell.2022.999351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023] Open
Abstract
Emerging and re-emerging respiratory viruses can spread rapidly and cause pandemics as demonstrated by the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The early human immune responses to respiratory viruses are in the nasal cavity and nasopharyngeal regions. Defining biomarkers of disease trajectory at the time of a positive diagnostic test would be an important tool to facilitate decisions such as initiation of antiviral treatment. We hypothesize that nasopharyngeal tRNA profiles could be used to predict Coronavirus Disease 19 (COVID-19) severity. We carried out multiplex small RNA sequencing (MSR-seq) on residual nasopharyngeal swabs to measure simultaneously full-length tRNA abundance, tRNA modifications, and tRNA fragmentation for the human tRNA response to SARS-CoV-2 infection. We identified distinct tRNA signatures associated with mild symptoms versus severe COVID-19 manifestations requiring hospitalization. These results highlight the utility of host tRNA properties as biomarkers for the clinical outcome of SARS-CoV-2.
Collapse
Affiliation(s)
- Christopher D. Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christopher P. Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Sihao Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Ana Gonzales-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| |
Collapse
|
325
|
Wang L, Hu X, Liu X, Feng Y, Zhang Y, Han J, Liu X, Meng F. m7G regulator-mediated methylation modification patterns define immune cell infiltration and patient survival. Front Immunol 2022; 13:1022720. [DOI: 10.3389/fimmu.2022.1022720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have demonstrated the important roles of epigenetic modifications in tumorigenesis, progression and prognosis. However, in hepatocellular carcinoma, the potential link between N7-methylguanosine (m7G) modification and molecular heterogeneity and tumor microenvironment (TME) remains unclear.MethodWe performed a comprehensive evaluation of m7G modification patterns in 816 hepatocellular carcinoma samples based on 24 m7G regulatory factors, identified different m7G modification patterns, and made a systematic correlation of these modification patterns with the infiltration characteristics of immunocytes. Then, we built and validated a scoring tool called m7G score.ResultsIn this study, we revealed the presence of three distinct m7G modification patterns in liver cancer, with remarkable differences in the immunocyte infiltration characteristics of these three subtypes. The m7G scoring system of this study could assess m7G modification patterns in individual hepatocellular carcinoma patients, could predict TME infiltration characteristics, genetic variants and patient prognosis. We also found that the m7G scoring system may be useful in guiding patients’ clinical use of medications.ConclusionsThis study revealed that m7G methylation modifications exerted a significant role in formation of TME in hepatocellular carcinoma. Assessing the m7G modification patterns of single patients would help enhance our perception of TME infiltration characteristics and give significant insights into immunotherapy efficacy.
Collapse
|
326
|
White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet 2022; 13:1037134. [PMID: 36386798 PMCID: PMC9650216 DOI: 10.3389/fgene.2022.1037134] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 06/26/2024] Open
Abstract
Next generation sequencing (NGS) has provided biologists with an unprecedented view into biological processes and their regulation over the past 2 decades, fueling a wave of development of high throughput methods based on short read DNA and RNA sequencing. For nucleic acid modifications, NGS has been coupled with immunoprecipitation, chemical treatment, enzymatic treatment, and/or the use of reverse transcriptase enzymes with fortuitous activities to enrich for and to identify covalent modifications of RNA and DNA. However, the majority of nucleic acid modifications lack commercial monoclonal antibodies, and mapping techniques that rely on chemical or enzymatic treatments to manipulate modification signatures add additional technical complexities to library preparation. Moreover, such approaches tend to be specific to a single class of RNA or DNA modification, and generate only indirect readouts of modification status. Third generation sequencing technologies such as the commercially available "long read" platforms from Pacific Biosciences and Oxford Nanopore Technologies are an attractive alternative for high throughput detection of nucleic acid modifications. While the former can indirectly sense modified nucleotides through changes in the kinetics of reverse transcription reactions, nanopore sequencing can in principle directly detect any nucleic acid modification that produces a signal distortion as the nucleic acid passes through a nanopore sensor embedded within a charged membrane. To date, more than a dozen endogenous DNA and RNA modifications have been interrogated by nanopore sequencing, as well as a number of synthetic nucleic acid modifications used in metabolic labeling, structure probing, and other emerging applications. This review is intended to introduce the reader to nanopore sequencing and key principles underlying its use in direct detection of nucleic acid modifications in unamplified DNA or RNA samples, and outline current approaches for detecting and quantifying nucleic acid modifications by nanopore sequencing. As this technology matures, we anticipate advances in both sequencing chemistry and analysis methods will lead to rapid improvements in the identification and quantification of these epigenetic marks.
Collapse
Affiliation(s)
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
| |
Collapse
|
327
|
McFeely CAL, Dods KK, Patel SS, Hartman MCT. Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA. Nucleic Acids Res 2022; 50:11374-11386. [PMID: 36300637 PMCID: PMC9638912 DOI: 10.1093/nar/gkac846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
Breaking codon degeneracy for the introduction of non-canonical amino acids offers many opportunities in synthetic biology. Yet, despite the existence of 64 codons, the code has only been expanded to 25 amino acids in vitro. A limiting factor could be the over-reliance on synthetic tRNAs which lack the post-transcriptional modifications that improve translational fidelity. To determine whether modified, wild-type tRNA could improve sense codon reassignment, we developed a new fluorous method for tRNA capture and applied it to the isolation of roughly half of the Escherichia coli tRNA isoacceptors. We then performed codon competition experiments between the five captured wild-type leucyl-tRNAs and their synthetic counterparts, revealing a strong preference for wild-type tRNA in an in vitro translation system. Finally, we compared the ability of wild-type and synthetic leucyl-tRNA to break the degeneracy of the leucine codon box, showing that only captured wild-type tRNAs are discriminated with enough fidelity to accurately split the leucine codon box for the encoding of three separate amino acids. Wild-type tRNAs are therefore enabling reagents for maximizing the reassignment potential of the genetic code.
Collapse
Affiliation(s)
- Clinton A L McFeely
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
- Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220 , USA
| | - Kara K Dods
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
- Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220 , USA
| | - Shivam S Patel
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
| | - Matthew C T Hartman
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
- Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220 , USA
| |
Collapse
|
328
|
Caldwell RM, Flynn RA. Discovering glycoRNA: Traditional and Non‐Canonical Approaches to Studying RNA Modifications. Isr J Chem 2022. [DOI: 10.1002/ijch.202200059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Reese M. Caldwell
- Stem Cell Program, Boston Children's Hospital Boston 02115 Massachusetts United States
- Stem Cell and Regenerative Biology Department, Harvard University Cambridage 02138 Massachusetts United States
| | - Ryan A. Flynn
- Stem Cell Program, Boston Children's Hospital Boston 02115 Massachusetts United States
- Stem Cell and Regenerative Biology Department, Harvard University Cambridage 02138 Massachusetts United States
| |
Collapse
|
329
|
Wang L, Lin S. Emerging functions of tRNA modifications in mRNA translation and diseases. J Genet Genomics 2022; 50:223-232. [PMID: 36309201 DOI: 10.1016/j.jgg.2022.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
tRNAs are essential modulators that recognize mRNA codons and bridge amino acids for mRNA translation. The tRNAs are heavily modified, which is essential for forming a complex secondary structure that facilitates codon recognition and mRNA translation. In recent years, studies have identified the regulatory roles of tRNA modifications in mRNA translation networks. Misregulation of tRNA modifications is closely related to the progression of developmental diseases and cancers. In this review, we summarize the tRNA biogenesis process and then discuss the effects and mechanisms of tRNA modifications on tRNA processing and mRNA translation. Finally, we provide a comprehensive overview of tRNA modifications' physiological and pathological functions, focusing on diseases including cancers.
Collapse
Affiliation(s)
- Lu Wang
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China; Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510080, China.
| |
Collapse
|
330
|
Cappannini A, Mosca K, Mukherjee S, Moafinejad S, Sinden R, Arluison V, Bujnicki J, Wien F. NACDDB: Nucleic Acid Circular Dichroism Database. Nucleic Acids Res 2022; 51:D226-D231. [PMID: 36280237 PMCID: PMC9825466 DOI: 10.1093/nar/gkac829] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/15/2022] [Indexed: 01/29/2023] Open
Abstract
The Nucleic Acid Circular Dichroism Database (NACDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data about nucleic acids, and the associated experimental metadata, structural models, and links to literature. NACDDB covers CD data for various nucleic acid molecules, including DNA, RNA, DNA/RNA hybrids, and various nucleic acid derivatives. The entries are linked to primary sequence and experimental structural data, as well as to the literature. Additionally, for all entries, 3D structure models are provided. All entries undergo expert validation and curation procedures to ensure completeness, consistency, and quality of the data included. The NACDDB is open for submission of the CD data for nucleic acids. NACDDB is available at: https://genesilico.pl/nacddb/.
Collapse
Affiliation(s)
| | | | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - S Naeim Moafinejad
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Richard R Sinden
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | | | | | - Frank Wien
- To whom correspondence should be addressed. Tel: +33 169359695;
| |
Collapse
|
331
|
Zhang X, Wang Y, Dong B, Jiang Y, Liu D, Xie K, Yu Y. Expression pattern and clinical value of Key RNA methylation modification regulators in ischemic stroke. Front Genet 2022; 13:1009145. [PMID: 36263422 PMCID: PMC9574037 DOI: 10.3389/fgene.2022.1009145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Ischemic stroke (IS) is one of the major causes of death and disability worldwide, and effective diagnosis and treatment methods are lacking. RNA methylation, a common epigenetic modification, plays an important role in disease progression. However, little is known about the role of RNA methylation modification in the regulation of IS. The aim of this study was to investigate RNA methylation modification patterns and immune infiltration characteristics in IS through bioinformatics analysis. We downloaded gene expression profiles of control and IS model rat brain tissues from the Gene Expression Omnibus database. IS profiles were divided into two subtypes based on RNA methylation regulators, and functional enrichment analyses were conducted to determine the differentially expressed genes (DEGs) between the subtypes. Weighted gene co-expression network analysis was used to explore co-expression modules and genes based on DEGs. The IS clinical diagnosis model was successfully constructed and four IS characteristic genes (GFAP, GPNMB, FKBP9, and CHMP5) were identified, which were significantly upregulated in IS samples. Characteristic genes were verified by receiver operating characteristic curve and real-time quantitative PCR analyses. The correlation between characteristic genes and infiltrating immune cells was determined by correlation analysis. Furthermore, GPNMB was screened using the protein-protein interaction network, and its regulatory network and the potential therapeutic drug chloroquine were predicted. Our finding describes the expression pattern and clinical value of key RNA methylation modification regulators in IS and novel diagnostic and therapeutic targets of IS from a new perspective.
Collapse
Affiliation(s)
- Xinyue Zhang
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Institute of Anesthesiology, Tianjin, China
| | - Yuanlin Wang
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Institute of Anesthesiology, Tianjin, China
| | - Beibei Dong
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Institute of Anesthesiology, Tianjin, China
| | - Yi Jiang
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Institute of Anesthesiology, Tianjin, China
| | - Dan Liu
- School of Medicine, Nankai University, Tianjin, China
| | - Keliang Xie
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Institute of Anesthesiology, Tianjin, China
- Department of Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yonghao Yu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Institute of Anesthesiology, Tianjin, China
- *Correspondence: Yonghao Yu,
| |
Collapse
|
332
|
Bessler L, Kaur N, Vogt LM, Flemmich L, Siebenaller C, Winz ML, Tuorto F, Micura R, Ehrenhofer-Murray AE, Helm M. Functional integration of a semi-synthetic azido-queuosine derivative into translation and a tRNA modification circuit. Nucleic Acids Res 2022; 50:10785-10800. [PMID: 36169220 PMCID: PMC9561289 DOI: 10.1093/nar/gkac822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/09/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Substitution of the queuine nucleobase precursor preQ1 by an azide-containing derivative (azido-propyl-preQ1) led to incorporation of this clickable chemical entity into tRNA via transglycosylation in vitro as well as in vivo in Escherichia coli, Schizosaccharomyces pombe and human cells. The resulting semi-synthetic RNA modification, here termed Q-L1, was present in tRNAs on actively translating ribosomes, indicating functional integration into aminoacylation and recruitment to the ribosome. The azide moiety of Q-L1 facilitates analytics via click conjugation of a fluorescent dye, or of biotin for affinity purification. Combining the latter with RNAseq showed that TGT maintained its native tRNA substrate specificity in S. pombe cells. The semi-synthetic tRNA modification Q-L1 was also functional in tRNA maturation, in effectively replacing the natural queuosine in its stimulation of further modification of tRNAAsp with 5-methylcytosine at position 38 by the tRNA methyltransferase Dnmt2 in S. pombe. This is the first demonstrated in vivo integration of a synthetic moiety into an RNA modification circuit, where one RNA modification stimulates another. In summary, the scarcity of queuosinylation sites in cellular RNA, makes our synthetic q/Q system a ‘minimally invasive’ system for placement of a non-natural, clickable nucleobase within the total cellular RNA.
Collapse
Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Navpreet Kaur
- Institute of Biology, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Laurin Flemmich
- Department of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Carmen Siebenaller
- Department of Chemistry - Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Marie-Luise Winz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ronald Micura
- Department of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | | | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| |
Collapse
|
333
|
He CM, Zhang XD, Zhu SX, Zheng JJ, Wang YM, Wang Q, Yin H, Fu YJ, Xue S, Tang J, Zhao XJ. Integrative pan-cancer analysis and clinical characterization of the N7-methylguanosine (m7G) RNA modification regulators in human cancers. Front Genet 2022; 13:998147. [PMID: 36226166 PMCID: PMC9549978 DOI: 10.3389/fgene.2022.998147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: RNA modification is one of the epigenetic mechanisms that regulates post-transcriptional gene expression, and abnormal RNA modifications have been reported to play important roles in tumorigenesis. N7-methylguanosine (m7G) is an essential modification at the 5′ cap of human mRNA. However, a systematic and pan-cancer analysis of the clinical relevance of m7G related regulatory genes is still lacking.Methods: We used univariate Cox model and Kaplan-Meier analysis to generate the forest plot of OS, PFI, DSS and identified the correlation between the altered expression of m7G regulators and patient survival in 33 cancer types from the TCGA and GTEx databases. Then, the “estimate” R-package, ssGSEA and CIBERSORT were used to depict the pan-cancer immune landscape. Through Spearman’s correlation test, we analyzed the correlation between m7G regulators and the tumor microenvironment (TME), immune subtype, and drug sensitivity of the tumors, which was further validated in NSCLC. We also assessed the changes in the expression of m7G related regulatory genes in NSCLC with regards to the genetic and transcriptional aspects and evaluated the correlation of METTL1 and WDR4 expression with TMB, MSI and immunotherapy in pan-cancer.Results: High expression of most of the m7G regulators was significantly associated with worse prognosis. Correlation analyses revealed that the expression of majority of the m7G regulators was correlated with tumor immune infiltration and tumor stem cell scores. Drug sensitivity analysis showed that the expression of CYFP1,2 was closely related to drug sensitivity for various anticancer agents (p < 0.001). Analysis of the pan-cancer immune subtype revealed significant differences in the expression of m7G regulators between different immune subtypes (p < 0.001). Additionally, the types and proportions of mutations in METTL1 and WDR4 and their relevance to immunotherapy were further described.Conclusion: Our study is the first to evaluate the correlation between the altered expression of m7G regulators and patient survival, the degree of immune infiltration, TME and drug sensitivity in pan-cancer datasets.
Collapse
Affiliation(s)
- Chun-Ming He
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xin-Di Zhang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Song-Xin Zhu
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jia-Jie Zheng
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Ming Wang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qing Wang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hang Yin
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Jie Fu
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Tang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Jian Tang, ; Xiao-Jing Zhao,
| | - Xiao-Jing Zhao
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Jian Tang, ; Xiao-Jing Zhao,
| |
Collapse
|
334
|
A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment. Noncoding RNA 2022; 8:ncrna8050063. [DOI: 10.3390/ncrna8050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Pseudouridylation is one of the most abundant modifications found in RNAs. To identify the Pseudouridylation sites (Psi) in RNAs, several techniques have been developed, but the most common and robust is the CMC (N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide) treatment, which consists in the addition of an adduct on Psi that inhibits the reverse transcription. Here, we describe a turnkey method and a tool to design the bridging oligo (DBO), which is somewhat difficult to design. Finally, we propose a trouble-shooting guide to help users.
Collapse
|
335
|
Katanski CD, Watkins CP, Zhang W, Reyer M, Miller S, Pan T. Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing. Nucleic Acids Res 2022; 50:e99. [PMID: 35713550 PMCID: PMC9508811 DOI: 10.1093/nar/gkac517] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
Collapse
Affiliation(s)
- Christopher D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Christopher P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Reyer
- Program of Biophysics, University of Chicago, Chicago, IL 60637, USA
| | - Samuel Miller
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
336
|
DLm6Am: A Deep-Learning-Based Tool for Identifying N6,2′-O-Dimethyladenosine Sites in RNA Sequences. Int J Mol Sci 2022; 23:ijms231911026. [PMID: 36232325 PMCID: PMC9570463 DOI: 10.3390/ijms231911026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/10/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
N6,2′-O-dimethyladenosine (m6Am) is a post-transcriptional modification that may be associated with regulatory roles in the control of cellular functions. Therefore, it is crucial to accurately identify transcriptome-wide m6Am sites to understand underlying m6Am-dependent mRNA regulation mechanisms and biological functions. Here, we used three sequence-based feature-encoding schemes, including one-hot, nucleotide chemical property (NCP), and nucleotide density (ND), to represent RNA sequence samples. Additionally, we proposed an ensemble deep learning framework, named DLm6Am, to identify m6Am sites. DLm6Am consists of three similar base classifiers, each of which contains a multi-head attention module, an embedding module with two parallel deep learning sub-modules, a convolutional neural network (CNN) and a Bi-directional long short-term memory (BiLSTM), and a prediction module. To demonstrate the superior performance of our model’s architecture, we compared multiple model frameworks with our method by analyzing the training data and independent testing data. Additionally, we compared our model with the existing state-of-the-art computational methods, m6AmPred and MultiRM. The accuracy (ACC) for the DLm6Am model was improved by 6.45% and 8.42% compared to that of m6AmPred and MultiRM on independent testing data, respectively, while the area under receiver operating characteristic curve (AUROC) for the DLm6Am model was increased by 4.28% and 5.75%, respectively. All the results indicate that DLm6Am achieved the best prediction performance in terms of ACC, Matthews correlation coefficient (MCC), AUROC, and the area under precision and recall curves (AUPR). To further assess the generalization performance of our proposed model, we implemented chromosome-level leave-out cross-validation, and found that the obtained AUROC values were greater than 0.83, indicating that our proposed method is robust and can accurately predict m6Am sites.
Collapse
|
337
|
The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer. Cell Mol Neurobiol 2022:10.1007/s10571-022-01283-8. [DOI: 10.1007/s10571-022-01283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/04/2022] [Indexed: 11/03/2022]
|
338
|
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.
Collapse
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
| |
Collapse
|
339
|
Fan Y, Li X, Sun H, Gao Z, Zhu Z, Yuan K. Role of WTAP in Cancer: From Mechanisms to the Therapeutic Potential. Biomolecules 2022; 12:biom12091224. [PMID: 36139062 PMCID: PMC9496264 DOI: 10.3390/biom12091224] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/16/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Wilms' tumor 1-associating protein (WTAP) is required for N6-methyladenosine (m6A) RNA methylation modifications, which regulate biological processes such as RNA splicing, cell proliferation, cell cycle, and embryonic development. m6A is the predominant form of mRNA modification in eukaryotes. WTAP exerts m6A modification by binding to methyltransferase-like 3 (METTL3) in the nucleus to form the METTL3-methyltransferase-like 14 (METTL14)-WTAP (MMW) complex, a core component of the methyltransferase complex (MTC), and localizing to the nuclear patches. Studies have demonstrated that WTAP plays a critical role in various cancers, both dependent and independent of its role in m6A modification of methyltransferases. Here, we describe the recent findings on the structural features of WTAP, the mechanisms by which WTAP regulates the biological functions, and the molecular mechanisms of its functions in various cancers. By summarizing the latest WTAP research, we expect to provide new directions and insights for oncology research and discover new targets for cancer treatment.
Collapse
Affiliation(s)
- Yongfei Fan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Xinwei Li
- Department of Gastroenterology, Affiliated Cancer Hospital of Bengbu Medical College, Bengbu 233000, China
| | - Huihui Sun
- Department of Radiotherapy, The Affiliated Changzhou No. 1 People’s Hospital of Suzhou University, Changzhou 213003, China
| | - Zhaojia Gao
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Zheng Zhu
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Kai Yuan
- Department of Thoracic Surgery, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Heart and Lung Disease Laboratory, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou 213003, China
- Correspondence:
| |
Collapse
|
340
|
Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ 1-Riboswitch. J Chem Inf Model 2022; 62:4134-4148. [PMID: 35994617 DOI: 10.1021/acs.jcim.2c00751] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.
Collapse
Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Simon Schneider
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Maike Grimm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| |
Collapse
|
341
|
Post-Transcriptional Modifications of RNA as Regulators of Apoptosis in Glioblastoma. Int J Mol Sci 2022; 23:ijms23169272. [PMID: 36012529 PMCID: PMC9408889 DOI: 10.3390/ijms23169272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
This review is devoted to changes in the post-transcriptional maturation of RNA in human glioblastoma cells, which leads to disruption of the normal course of apoptosis in them. The review thoroughly highlights the latest information on both post-transcriptional modifications of certain regulatory RNAs, associated with the process of apoptosis, presents data on the features of apoptosis in glioblastoma cells, and shows the relationship between regulatory RNAs and the apoptosis in tumor cells. In conclusion, potential target candidates are presented that are necessary for the development of new drugs for the treatment of glioblastoma.
Collapse
|
342
|
RNA Modifications in Gastrointestinal Cancer: Current Status and Future Perspectives. Biomedicines 2022; 10:biomedicines10081918. [PMID: 36009465 PMCID: PMC9405978 DOI: 10.3390/biomedicines10081918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 01/05/2023] Open
Abstract
Gastrointestinal (GI) cancer, referring to cancers of the digestive system such as colorectal cancer (CRC), gastric cancer (GC), and liver cancer, is a major cause of cancer-related deaths in the world. A series of genetic, epigenetic, and epitranscriptomic changes occur during the development of GI cancer. The identification of these molecular events provides potential diagnostic, prognostic, and therapeutic targets for cancer patients. RNA modification is required in the posttranscriptional regulation of RNA metabolism, including splicing, intracellular transport, degradation, and translation. RNA modifications such as N6-methyladenosine (m6A) and N1-methyladenosine (m1A) are dynamically regulated by three different types of regulators named methyltransferases (writers), RNA binding proteins (readers), and demethylases (erasers). Recent studies have pointed out that abnormal RNA modification contributes to GI tumorigenesis and progression. In this review, we summarize the latest findings on the functional significance of RNA modification in GI cancer and discuss the therapeutic potential of epitranscriptomic inhibitors for cancer treatment.
Collapse
|
343
|
Blaze J, Akbarian S. The tRNA regulome in neurodevelopmental and neuropsychiatric disease. Mol Psychiatry 2022; 27:3204-3213. [PMID: 35505091 PMCID: PMC9630165 DOI: 10.1038/s41380-022-01585-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/14/2022]
Abstract
Transfer (t)RNAs are 70-90 nucleotide small RNAs highly regulated by 43 different types of epitranscriptomic modifications and requiring aminoacylation ('charging') for mRNA decoding and protein synthesis. Smaller cleavage products of mature tRNAs, or tRNA fragments, have been linked to a broad variety of noncanonical functions, including translational inhibition and modulation of the immune response. Traditionally, knowledge about tRNA regulation in brain is derived from phenotypic exploration of monogenic neurodevelopmental and neurodegenerative diseases associated with rare mutations in tRNA modification genes. More recent studies point to the previously unrecognized potential of the tRNA regulome to affect memory, synaptic plasticity, and affective states. For example, in mature cortical neurons, cytosine methylation sensitivity of the glycine tRNA family (tRNAGly) is coupled to glycine biosynthesis and codon-specific alterations in ribosomal translation together with robust changes in cognition and depression-related behaviors. In this Review, we will discuss the emerging knowledge of the neuronal tRNA landscape, with a focus on epitranscriptomic tRNA modifications and downstream molecular pathways affected by alterations in tRNA expression, charging levels, and cleavage while mechanistically linking these pathways to neuropsychiatric disease and provide insight into future areas of study for this field.
Collapse
Affiliation(s)
- Jennifer Blaze
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Schahram Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
344
|
Gosset-Erard C, Lechner A, Wolff P, Aubriet F, Leize-Wagner E, Chaimbault P, François YN. Optimization of nucleotides dephosphorylation for RNA structural characterization by tandem mass spectrometry hyphenated with separation methods. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1208:123396. [PMID: 35917777 DOI: 10.1016/j.jchromb.2022.123396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022]
Abstract
As part of RNA characterization, the identification of post-transcriptional modifications can be performed using hyphenation of separation methods with mass spectrometry. To identify RNA modifications with those methods, a first total digestion followed by a dephosphorylation step are usually required to reduce RNA to nucleosides. Even though effective digestion and dephosphorylation are essential to avoid further complications in analysis and data interpretation, to our knowledge, no standard protocol is yet referenced in the literature. Therefore, the aim of this work is to optimize the dephosphorylation step using a total extract of transfer RNA (tRNA)1 from B. taurus as a model and to determine and fix two protocols, leading to complete dephosphorylation, based on time and bacterial alkaline phosphatase (BAP)2 consumptions. Capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) was used to estimate the dephosphorylation efficiency of both protocols on many canonical and modified nucleotides. For a timesaving protocol, we established that full dephosphorylation was obtained after a 4-hour incubation at 37 °C with 7.5 U of BAP for 1 µg of tRNA. And for a BAP-saving protocol, we established that full dephosphorylation was obtained 3.0 U of BAP after an overnight incubation at 37 °C. Both protocols are suitable for quantitative analyses as no loss of analytes is expected. Moreover, they can be widely used for all other RNA classes, including messenger RNA or ribosomal RNA.
Collapse
Affiliation(s)
- Clarisse Gosset-Erard
- Université de Lorraine, LCP-A2MC, F-57000 Metz, France; Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| | - Antony Lechner
- Architecture et Réactivité de l'ARN (ARN) UPR 9002, CNRS, Université de Strasbourg, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade FRC 1589, CNRS, Strasbourg, France.
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN (ARN) UPR 9002, CNRS, Université de Strasbourg, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade FRC 1589, CNRS, Strasbourg, France.
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| | | | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| |
Collapse
|
345
|
Mersinoglu B, Cristinelli S, Ciuffi A. The Impact of Epitranscriptomics on Antiviral Innate Immunity. Viruses 2022; 14:v14081666. [PMID: 36016289 PMCID: PMC9412694 DOI: 10.3390/v14081666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Epitranscriptomics, i.e., chemical modifications of RNA molecules, has proven to be a new layer of modulation and regulation of protein expression, asking for the revisiting of some aspects of cellular biology. At the virological level, epitranscriptomics can thus directly impact the viral life cycle itself, acting on viral or cellular proteins promoting replication, or impacting the innate antiviral response of the host cell, the latter being the focus of the present review.
Collapse
|
346
|
Chen HM, Li H, Lin MX, Fan WJ, Zhang Y, Lin YT, Wu SX. Research Progress for RNA Modifications in Physiological and Pathological Angiogenesis. Front Genet 2022; 13:952667. [PMID: 35937999 PMCID: PMC9354963 DOI: 10.3389/fgene.2022.952667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
As a critical layer of epigenetics, RNA modifications demonstrate various molecular functions and participate in numerous biological processes. RNA modifications have been shown to be essential for embryogenesis and stem cell fate. As high-throughput sequencing and antibody technologies advanced by leaps and bounds, the association of RNA modifications with multiple human diseases sparked research enthusiasm; in addition, aberrant RNA modification leads to tumor angiogenesis by regulating angiogenesis-related factors. This review collected recent cutting-edge studies focused on RNA modifications (N6-methyladenosine (m6A), N5-methylcytosine (m5C), N7-methylguanosine (m7G), N1-methyladenosine (m1A), and pseudopuridine (Ψ)), and their related regulators in tumor angiogenesis to emphasize the role and impact of RNA modifications.
Collapse
Affiliation(s)
- Hui-Ming Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Hang Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Meng-Xian Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wei-Jie Fan
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yi Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yan-Ting Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Shu-Xiang Wu, ; Yan-Ting Lin,
| | - Shu-Xiang Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Shu-Xiang Wu, ; Yan-Ting Lin,
| |
Collapse
|
347
|
del Valle-Morales D, Le P, Saviana M, Romano G, Nigita G, Nana-Sinkam P, Acunzo M. The Epitranscriptome in miRNAs: Crosstalk, Detection, and Function in Cancer. Genes (Basel) 2022; 13:genes13071289. [PMID: 35886072 PMCID: PMC9316458 DOI: 10.3390/genes13071289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
The epitranscriptome encompasses all post-transcriptional modifications that occur on RNAs. These modifications can alter the function and regulation of their RNA targets, which, if dysregulated, result in various diseases and cancers. As with other RNAs, miRNAs are highly modified by epitranscriptomic modifications such as m6A methylation, 2′-O-methylation, m5C methylation, m7G methylation, polyuridine, and A-to-I editing. miRNAs are a class of small non-coding RNAs that regulates gene expression at the post-transcriptional level. miRNAs have gathered high clinical interest due to their role in disease, development, and cancer progression. Epitranscriptomic modifications alter the targeting, regulation, and biogenesis of miRNAs, increasing the complexity of miRNA regulation. In addition, emerging studies have revealed crosstalk between these modifications. In this review, we will summarize the epitranscriptomic modifications—focusing on those relevant to miRNAs—examine the recent crosstalk between these modifications, and give a perspective on how this crosstalk expands the complexity of miRNA biology.
Collapse
Affiliation(s)
- Daniel del Valle-Morales
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Michela Saviana
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giovanni Nigita
- Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
- Correspondence:
| |
Collapse
|
348
|
Qin S, Zhang Q, Xu Y, Ma S, Wang T, Huang Y, Ju S. m 6A-modified circRNAs: detections, mechanisms, and prospects in cancers. Mol Med 2022; 28:79. [PMID: 35836125 PMCID: PMC9284916 DOI: 10.1186/s10020-022-00505-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) have become a research hotspot in recent years with their universality, diversity, stability, conservativeness, and spatiotemporal specificity. N6-methyladenosine (m6A), the most abundant modification in the eukaryotic cells, is engaged in the pathophysiological processes of various diseases. An increasing amount of evidence has suggested that m6A modification is common in circRNAs and is associated with their biological functions. This review summarizes the effects of m6A modification on circRNAs and their regulation mechanisms in cancers, providing some suggestions of m6A-modified circRNAs in cancer therapy.
Collapse
Affiliation(s)
- Shiyi Qin
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Qi Zhang
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Yanhua Xu
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Shuo Ma
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Tianyi Wang
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China. .,Department of Medical Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226001, Jiangsu, China. .,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.
| |
Collapse
|
349
|
The Role of RNA Modification in HIV-1 Infection. Int J Mol Sci 2022; 23:ijms23147571. [PMID: 35886919 PMCID: PMC9317671 DOI: 10.3390/ijms23147571] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 01/25/2023] Open
Abstract
RNA plays an important role in biology, and more than 170 RNA modifications have been identified so far. Post-transcriptional modification of RNA in cells plays a crucial role in the regulation of its stability, transport, processing, and gene expression. So far, the research on RNA modification and the exact role of its enzymes is becoming more and more comprehensive. Human immunodeficiency virus 1 (HIV-1) is an RNA virus and the causative agent of acquired immunodeficiency syndrome (AIDS), which is one of the most devastating viral pandemics in history. More and more studies have shown that HIV has RNA modifications and regulation of its gene expression during infection and replication. This review focuses on several RNA modifications and their regulatory roles as well as the roles that different RNA modifications play during HIV-1 infection, in order to find new approaches for the development of anti-HIV-1 therapeutics.
Collapse
|
350
|
Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
Collapse
|