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Baquero-Pérez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson SA, Novoa EM, Díez J. N 6-methyladenosine modification is not a general trait of viral RNA genomes. Nat Commun 2024; 15:1964. [PMID: 38467633 PMCID: PMC10928186 DOI: 10.1038/s41467-024-46278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-Seq, an antibody-dependent technique with a high rate of false positives. Here, we address the presence of m6A in CHIKV and DENV RNAs. For this, we combine m6A-Seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we find no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery does not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection has no effect on the m6A machinery's localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.
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Affiliation(s)
- Belinda Baquero-Pérez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ivaylo D Yonchev
- Sheffield Institute for Nucleic Acids (SInFoNiA) and School of Biosciences, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anna Delgado-Tejedor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Rebeca Medina
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Mireia Puig-Torrents
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ian Sudbery
- Sheffield Institute for Nucleic Acids (SInFoNiA) and School of Biosciences, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Oguzhan Begik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Stuart A Wilson
- Sheffield Institute for Nucleic Acids (SInFoNiA) and School of Biosciences, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
| | - Juana Díez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain.
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2
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Ma HL, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang MK, Yoshimi A, Lin KT, Riching KM, Wang X, Beckman JI, Arya S, Droin N, Calonne E, Hassabi B, Zhang QY, Li A, Putmans P, Malbec L, Hubert C, Lan J, Mies F, Yang Y, Solary E, Daniels DL, Gupta YK, Deplus R, Abdel-Wahab O, Yang YG, Fuks F. SRSF2 plays an unexpected role as reader of m 5C on mRNA, linking epitranscriptomics to cancer. Mol Cell 2023; 83:4239-4254.e10. [PMID: 38065062 PMCID: PMC11090011 DOI: 10.1016/j.molcel.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here, we identify serine/arginine-rich splicing factor 2 (SRSF2) as a reader of m5C and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.
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Affiliation(s)
- Hai-Li Ma
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Christelle Soares Da Costa
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédéric Murisier
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Eric James de Bony
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Meng-Ke Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Akihide Yoshimi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Xing Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - John I Beckman
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nathalie Droin
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Qing-Yang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Lionel Malbec
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Céline Hubert
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Eric Solary
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | | | - Yogesh K Gupta
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium.
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Yang Y, Liu Z, Lu J, Sun Y, Fu Y, Pan M, Xie X, Ge Q. Analysis approaches for the identification and prediction of N6-methyladenosine sites. Epigenetics 2023; 18:2158284. [PMID: 36562485 PMCID: PMC9980620 DOI: 10.1080/15592294.2022.2158284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m6A sites, in particular full-transcriptome m6A. And individual m6A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m6A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m6A methylation, including the experimental detection of m6A methylation sites, techniques of data analysis, the way of predicting m6A methylation sites, m6A methylation databases, and detection of m6A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.
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Affiliation(s)
- Yuwei Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Junru Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yuqing Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yue Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Min Pan
- Department of Pathology and Pathophysiology School of Medicine, Southeast University, Nanjing, China
| | - Xueying Xie
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
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4
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Meng Q, Schatten H, Zhou Q, Chen J. Crosstalk between m6A and coding/non-coding RNA in cancer and detection methods of m6A modification residues. Aging (Albany NY) 2023; 15:6577-6619. [PMID: 37437245 PMCID: PMC10373953 DOI: 10.18632/aging.204836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
N6-methyladenosine (m6A) is one of the most common and well-known internal RNA modifications that occur on mRNAs or ncRNAs. It affects various aspects of RNA metabolism, including splicing, stability, translocation, and translation. An abundance of evidence demonstrates that m6A plays a crucial role in various pathological and biological processes, especially in tumorigenesis and tumor progression. In this article, we introduce the potential functions of m6A regulators, including "writers" that install m6A marks, "erasers" that demethylate m6A, and "readers" that determine the fate of m6A-modified targets. We have conducted a review on the molecular functions of m6A, focusing on both coding and noncoding RNAs. Additionally, we have compiled an overview of the effects noncoding RNAs have on m6A regulators and explored the dual roles of m6A in the development and advancement of cancer. Our review also includes a detailed summary of the most advanced databases for m6A, state-of-the-art experimental and sequencing detection methods, and machine learning-based computational predictors for identifying m6A sites.
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Affiliation(s)
- Qingren Meng
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, The Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Qian Zhou
- International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong Province, China
| | - Jun Chen
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, The Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, Guangdong Province, China
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5
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Baron F, Zhang M, Archer N, Bellows E, Knight HM, Welham S, Rutland CS, Mongan NP, Hayes CJ, Fray RG, Bodi Z. The importance of m 6A topology in chicken embryo mRNA: a precise mapping of m 6A at the conserved chicken β-actin zipcode. RNA (NEW YORK, N.Y.) 2023; 29:777-789. [PMID: 36810234 PMCID: PMC10187669 DOI: 10.1261/rna.079615.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 05/18/2023]
Abstract
N6-methyladenosine (m6A) in mRNA regulates almost every stage in the mRNA life cycle, and the development of methodologies for the high-throughput detection of methylated sites in mRNA using m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIPSeq) or m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) have revolutionized the m6A research field. Both of these methods are based on immunoprecipitation of fragmented mRNA. However, it is well documented that antibodies often have nonspecific activities, thus verification of identified m6A sites using an antibody-independent method would be highly desirable. We mapped and quantified the m6A site in the chicken β-actin zipcode based on the data from chicken embryo MeRIPSeq results and our RNA-Epimodification Detection and Base-Recognition (RedBaron) antibody-independent assay. We also demonstrated that methylation of this site in the β-actin zipcode enhances ZBP1 binding in vitro, while methylation of a nearby adenosine abolishes binding. This suggests that m6A may play a role in regulating localized translation of β-actin mRNA, and the ability of m6A to enhance or inhibit a reader protein's RNA binding highlights the importance of m6A detection at nucleotide resolution.
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Affiliation(s)
- Francis Baron
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Mi Zhang
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Nathan Archer
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Eleanor Bellows
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Helen M Knight
- Faculty of Medicine and Health Sciences, Queen's Medical Center, Nottingham NG7 2UH, United Kingdom
| | - Simon Welham
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Christopher J Hayes
- School of Chemistry, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Rupert G Fray
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Zsuzsa Bodi
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
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6
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Shinde H, Dudhate A, Kadam US, Hong JC. RNA methylation in plants: An overview. FRONTIERS IN PLANT SCIENCE 2023; 14:1132959. [PMID: 36938064 PMCID: PMC10014531 DOI: 10.3389/fpls.2023.1132959] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
RNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasingly clear. However, RNA methylation in plants is still poorly understood. Recently, plant science research on RNA methylation has advanced rapidly, and it has become clear that RNA methylation plays a critical role in plant development. This review summarizes current knowledge on RNA methylation in plant development. Plant writers, erasers, and readers are highlighted, as well as the occurrence, methods, and software development in RNA methylation is summarized. The most common and abundant RNA methylation in plants is N6-methyladenosine (m6A). In Arabidopsis, mutations in writers, erasers, and RNA methylation readers have affected the plant's phenotype. It has also been demonstrated that methylated TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1-messenger RNA moves from shoot to root while unmethylated TCTP1-mRNA does not. Methylated RNA immunoprecipitation, in conjunction with next-generation sequencing, has been a watershed moment in plant RNA methylation research. This method has been used successfully in rice, Arabidopsis, Brassica, and maize to study transcriptome-wide RNA methylation. Various software or tools have been used to detect methylated RNAs at the whole transcriptome level; the majority are model-based analysis tools (for example, MACS2). Finally, the limitations and future prospects of methylation of RNA research have been documented.
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Affiliation(s)
- Harshraj Shinde
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Ambika Dudhate
- Sequencing and Genome Discovery Center, Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Ulhas S. Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju-daero, Jinju, Gyeongnam, Republic of Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju-daero, Jinju, Gyeongnam, Republic of Korea
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
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7
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Abstract
The epitranscriptome, defined as RNA modifications that do not involve alterations in the nucleotide sequence, is a popular topic in the genomic sciences. Because we need massive computational techniques to identify epitranscriptomes within individual transcripts, many tools have been developed to infer epitranscriptomic sites as well as to process datasets using high-throughput sequencing. In this review, we summarize recent developments in epitranscriptome spatial detection and data analysis and discuss their progression.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
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8
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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.
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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.)
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9
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He X, Zhang L, Liu S, Wang J, Liu Y, Xiong A, Jiang M, Luo L, Ying X, Li G. Methyltransferase-like 3 leads to lung injury by up-regulation of interleukin 24 through N6-methyladenosine-dependent mRNA stability and translation efficiency in mice exposed to fine particulate matter 2.5. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119607. [PMID: 35718042 DOI: 10.1016/j.envpol.2022.119607] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Fine particulate matter 2.5 (PM2.5) exposure leads to the progress of pulmonary disease. It has been reported that N6-methyladenosine (m6A) modification was involved in various biological processes and diseases. However, the critical role of m6A modification in pulmonary disease during PM2.5 exposure remains elusive. Here, we revealed that lung inflammation and mucus production caused by PM2.5 were associated with m6A modification. Both in vivo and in vitro assays demonstrated that PM2.5 exposure elevated the total level of m6A modification as well as the methyltransferase like 3 (METTL3) expression. Integration analysis of m6A RNA immunoprecipitation-seq (meRIP-seq) and RNA-seq discovered that METTL3 up-regulated the expression level and the m6A modification of Interleukin 24 (IL24). Importantly, we explored that the stability of IL24 mRNA was enhanced due to the increased m6A modification. Moreover, the data from qRT-PCR showed that PM2.5 also increased YTH N6-Methyladenosine RNA Binding Protein 1 (YTHDF1) expression, and the up-regulated YTHDF1 augmented IL24 mRNA translation efficiency. Down-regulation of Mettl3 reduced Il24 expression and ameliorated the pulmonary inflammation and mucus secretion in mice exposed to PM2.5. Taken together, our finding provided a comprehensive insight for revealing the significant role of m6A regulators in the lung injury via METTL3/YTHDF1-coupled epitranscriptomal regulation of IL24.
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Affiliation(s)
- Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Lei Zhang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Shengbin Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Junyi Wang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Yao Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Anying Xiong
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Manling Jiang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Li Luo
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China
| | - Xiong Ying
- Department of Pulmonary and Critical Care Medicine, Sichuan Friendship Hospital, Chengdu, 610000, China
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, 610031, China.
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10
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Ma L, He LN, Kang S, Gu B, Gao S, Zuo Z. Advances in detecting N6-methyladenosine modification in circRNAs. Methods 2022; 205:234-246. [PMID: 35878749 DOI: 10.1016/j.ymeth.2022.07.011] [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: 06/18/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with covalently single-stranded closed loop structures derived from back-splicing event of linear precursor mRNAs (pre-mRNAs). N6-methyladenosine (m6A), the most abundant epigenetic modification in eukaryotic RNAs, has been shown to play a crucial role in regulating the fate and biological function of circRNAs, and thus affecting various physiological and pathological processes. Accurate identification of m6A modification in circRNAs is an essential step to fully elucidate the crosstalk between m6A and circRNAs. In recent years, the rapid development of high-throughput sequencing technology and bioinformatic methodology has propelled the establishment of a multitude of approaches to detect circRNAs and m6A modification, including in vitro-based and in silico methods. Based on this, the research community has started on a new journey to develop methods for identification of m6A modification in circRNAs. In this review, we provide a comprehensive review and evaluation of the existing methods responsible for detecting circRNAs, m6A modification, and especially, m6A modification in circRNAs, which mainly focused on those developed based on high-throughput technologies and methodology of bioinformatics. This handy reference can help researchers figure out towards which direction this field will go.
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Affiliation(s)
- Lixia Ma
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Li-Na He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shiyang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Bianli Gu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Shegan Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China.
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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11
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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.
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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.
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12
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Li N, Rana TM. Detection of N6-methyladenosine in SARS-CoV-2 RNA by methylated RNA immunoprecipitation sequencing. STAR Protoc 2022; 3:101067. [PMID: 34901888 PMCID: PMC8651518 DOI: 10.1016/j.xpro.2021.101067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
N 6 -methylation of adenosine (m6A) is the most abundant internal mRNA modification and is an important post-transcriptional regulator of gene expression. Here, we describe a protocol for methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to detect and quantify m6A modifications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. The protocol is optimized for low viral RNA levels and is readily adaptable for other applications. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).
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Affiliation(s)
- Na Li
- Division of Genetics, Department of Pediatrics, Program in Immunology, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Tariq M. Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
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13
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Two zinc finger proteins with functions in m 6A writing interact with HAKAI. Nat Commun 2022; 13:1127. [PMID: 35236848 PMCID: PMC8891334 DOI: 10.1038/s41467-022-28753-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/09/2022] [Indexed: 12/30/2022] Open
Abstract
The methyltransferase complex (m6A writer), which catalyzes the deposition of N6-methyladenosine (m6A) in mRNAs, is highly conserved across most eukaryotic organisms, but its components and interactions between them are still far from fully understood. Here, using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, are discovered as components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA (mRNA adenosine methylase A). Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation and decreased lateral root formation. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ2 is likely the plant equivalent of ZC3H13 (Flacc) of the metazoan m6A-METTL Associated Complex. The components of m6A writer and their interactions are still far from fully understood. Here, the authors identify two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, as components of the Arabidopsis m6A writer complex, and show that hiz2 mutant plants have an 85% reduction in m6A abundance and severe developmental defects.
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14
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Zhou Y, Yang J, Tian Z, Zeng J, Shen W. Research progress concerning m 6A methylation and cancer. Oncol Lett 2021; 22:775. [PMID: 34589154 PMCID: PMC8442141 DOI: 10.3892/ol.2021.13036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) methylation is a type of methylation modification on RNA molecules, which was first discovered in 1974, and has become a hot topic in life science in recent years. m6A modification is an epigenetic regulation similar to DNA and histone modification and is dynamically reversible in mammalian cells. This chemical marker of RNA is produced by m6A 'writers' (methylase) and can be degraded by m6A 'erasers' (demethylase). Methylated reading protein is the 'reader', that can recognize the mRNA containing m6A and regulate the expression of downstream genes accordingly. m6A methylation is involved in all stages of the RNA life cycle, including RNA processing, nuclear export, translation and regulation of RNA degradation, indicating that m6A plays a crucial role in RNA metabolism. Recent studies have shown that m6A modification is a complicated regulatory network in different cell lines, tissues and spatio-temporal models, and m6A methylation is associated with the occurrence and development of tumors. The present review describes the regulatory mechanism and physiological functions of m6A methylation, and its research progress in several types of human tumor, to provide novel approaches for early diagnosis and targeted treatment of cancer.
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Affiliation(s)
- Yang Zhou
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jie Yang
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Zheng Tian
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jing Zeng
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Weigan Shen
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
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15
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RNA m 6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. Cell Res 2021; 31:861-885. [PMID: 34108665 PMCID: PMC8324889 DOI: 10.1038/s41422-021-00515-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The molecular basis underlying the interaction between retrotransposable elements (RTEs) and the human genome remains poorly understood. Here, we profiled N6-methyladenosine (m6A) deposition on nascent RNAs in human cells by developing a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m6A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes, and are bound by a dozen RNA binding proteins (RBPs) that are putative novel readers of m6A-modified RNAs, including a nuclear matrix protein SAFB. Notably, m6A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes with critical roles in DNA damage repair and sometimes in L1 suppression per se, where they act as transcriptional "roadblocks" to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m6A-L1s to reduce their levels, and to safeguard hosting gene transcription. Remarkably, our analysis identified thousands of MILs in multiple human fetal tissues, enlisting them as a novel category of cell-type-specific regulatory elements that often compromise transcription of long genes and confer their vulnerability in neurodevelopmental disorders. We propose that this m6A-orchestrated L1-host interaction plays widespread roles in gene regulation, genome integrity, human development and diseases.
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16
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Wang Q, Liang Y, Luo X, Liu Y, Zhang X, Gao L. N6-methyladenosine RNA modification: A promising regulator in central nervous system injury. Exp Neurol 2021; 345:113829. [PMID: 34339678 DOI: 10.1016/j.expneurol.2021.113829] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/08/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022]
Abstract
In addition to DNA methylation, reversible epigenetic modification occurring in RNA has been discovered recently. The most abundant type of RNA methylation is N6-methyladenosine (m6A) modification, which is dynamically regulated by methylases ("writers"), demethylases ("erasers") and m6A-binding proteins ("readers"). As an essential posttranscriptional regulator, m6A can control mRNA splicing, processing, stability, export and translation. Recent studies have revealed that m6A modification has the strongest tissue specificity for brain tissue and plays crucial roles in central nervous system (CNS) injures by affecting its downstream target genes or non-coding RNAs. This review focuses on the expression and function of m6A regulatory proteins in CNS trauma in vitro and in vivo. We also highlight the latest insights into the molecular mechanisms of pathological damage in the CNS. Understanding m6A dynamics, functions, and machinery will yield an opportunity for designing and developing novel therapeutic agents for CNS injuries.
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Affiliation(s)
- Qiang Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China; Department of Immunology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yundan Liang
- Department of Pathology and Pathophysiology, Chengdu Medical College, Chengdu, Sichuan 610500, PR China
| | - Xiaolei Luo
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yuqing Liu
- Laboratory of Metabolomics and Gynecological Disease Research, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China
| | - Xiaoli Zhang
- Laboratory of Metabolomics and Gynecological Disease Research, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China
| | - Linbo Gao
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China.
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17
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From A to m 6A: The Emerging Viral Epitranscriptome. Viruses 2021; 13:v13061049. [PMID: 34205979 PMCID: PMC8227502 DOI: 10.3390/v13061049] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/18/2022] Open
Abstract
There are over 100 different chemical RNA modifications, collectively known as the epitranscriptome. N6-methyladenosine (m6A) is the most commonly found internal RNA modification in cellular mRNAs where it plays important roles in the regulation of the mRNA structure, stability, translation and nuclear export. This modification is also found in viral RNA genomes and in viral mRNAs derived from both RNA and DNA viruses. A growing body of evidence indicates that m6A modifications play important roles in regulating viral replication by interacting with the cellular m6A machinery. In this review, we will exhaustively detail the current knowledge on m6A modification, with an emphasis on its function in virus biology.
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18
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Chen H, Gao S, Liu W, Wong CC, Wu J, Wu J, Liu D, Gou H, Kang W, Zhai J, Li C, Su H, Wang S, Soares F, Han J, He HH, Yu J. RNA N 6-Methyladenosine Methyltransferase METTL3 Facilitates Colorectal Cancer by Activating the m 6A-GLUT1-mTORC1 Axis and Is a Therapeutic Target. Gastroenterology 2021; 160:1284-1300.e16. [PMID: 33217448 DOI: 10.1053/j.gastro.2020.11.013] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS RNA N6-methyladenosine (m6A) modification has recently emerged as a new regulatory mechanism in cancer progression. We aimed to explore the role of the m6A regulatory enzyme METTL3 in colorectal cancer (CRC) pathogenesis and its potential as a therapeutic target. METHODS The expression and clinical implication of METTL3 were investigated in multiple human CRC cohorts. The underlying mechanisms of METTL3 in CRC were investigated by integrative m6A sequencing, RNA sequencing, and ribosome profiling analyses. The efficacy of targeting METTL3 in CRC treatment was elucidated in CRC cell lines, patient-derived CRC organoids, and Mettl3-knockout mouse models. RESULTS Using targeted clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 dropout screening, we identified METTL3 as the top essential m6A regulatory enzyme in CRC. METTL3 was overexpressed in 62.2% (79/127) and 88.0% (44/50) of primary CRCs from 2 independent cohorts. High METTL3 expression predicted poor survival in patients with CRC (n = 374, P < .01). Functionally, silencing METTL3 suppressed tumorigenesis in CRC cells, human-derived primary CRC organoids, and Mettl3-knockout mouse models. We discovered the novel functional m6A methyltransferase domain of METTL3 in CRC cells by domain-focused CRISPR screening and mutagenesis assays. Mechanistically, METTL3 directly induced the m6A-GLUT1-mTORC1 axis as identified by integrated m6A sequencing, RNA sequencing, ribosome sequencing, and functional validation. METTL3 induced GLUT1 translation in an m6A-dependent manner, which subsequently promoted glucose uptake and lactate production, leading to the activation of mTORC1 signaling and CRC development. Furthermore, inhibition of mTORC1 potentiated the anticancer effect of METTL3 silencing in CRC patient-derived organoids and METTL3 transgenic mouse models. CONCLUSIONS METTL3 promotes CRC by activating the m6A-GLUT1-mTORC1 axis. METTL3 is a promising therapeutic target for the treatment of CRC.
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Affiliation(s)
- Huarong Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Shanshan Gao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Weixin Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Chi-Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jingtong Wu
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, China
| | - Dabin Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Hongyan Gou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Jianning Zhai
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Chuangen Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Hao Su
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Shiyan Wang
- Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, China
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
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19
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Shafik AM, Zhang F, Guo Z, Dai Q, Pajdzik K, Li Y, Kang Y, Yao B, Wu H, He C, Allen EG, Duan R, Jin P. N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease. Genome Biol 2021; 22:17. [PMID: 33402207 PMCID: PMC7786910 DOI: 10.1186/s13059-020-02249-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification is known to impact many aspects of RNA metabolism, including mRNA stability and translation, and is highly prevalent in the brain. RESULTS We show that m6A modification displays temporal and spatial dynamics during neurodevelopment and aging. Genes that are temporally differentially methylated are more prone to have mRNA expression changes and affect many pathways associated with nervous system development. Furthermore, m6A shows a distinct tissue-specific methylation profile, which is most pronounced in the hypothalamus. Tissue-specific methylation is associated with an increase in mRNA expression and is associated with tissue-specific developmental processes. During the aging process, we observe significantly more m6A sites as age increases, in both mouse and human. We show a high level of overlap between mouse and human; however, humans at both young and old ages consistently show more m6A sites compared to mice. Differential m6A sites are found to be enriched in alternative untranslated regions of genes that affect aging-related pathways. These m6A sites are associated with a strong negative effect on mRNA expression. We also show that many Alzheimer-related transcripts exhibit decreased m6A methylation in a mouse model of Alzheimer's disease, which is correlated with reduced protein levels. CONCLUSIONS Our results suggest that m6A exerts a critical function in both early and late brain development in a spatio-temporal fashion. Furthermore, m6A controls protein levels of key genes involved in Alzheimer's disease-associated pathways, suggesting that m6A plays an important role in aging and neurodegenerative disease.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Feiran Zhang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Zhenxing Guo
- Department of Biostatistics and Bioinformatics, School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Kinga Pajdzik
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Yangping Li
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Yunhee Kang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Bing Yao
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Ranhui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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20
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Lu Z, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY. Structural modularity of the XIST ribonucleoprotein complex. Nat Commun 2020; 11:6163. [PMID: 33268787 PMCID: PMC7710737 DOI: 10.1038/s41467-020-20040-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.
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Affiliation(s)
- Zhipeng Lu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Brian Zarnegar
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Qing Ma
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Synthetic Biology Department, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, PR China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Fan Liu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Hani Choudhry
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, 22252, Saudi Arabia
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
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21
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Liu L, Song B, Ma J, Song Y, Zhang SY, Tang Y, Wu X, Wei Z, Chen K, Su J, Rong R, Lu Z, de Magalhães JP, Rigden DJ, Zhang L, Zhang SW, Huang Y, Lei X, Liu H, Meng J. Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. Comput Struct Biotechnol J 2020; 18:1587-1604. [PMID: 32670500 PMCID: PMC7334300 DOI: 10.1016/j.csbj.2020.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional RNA modification occurs on all types of RNA and plays a vital role in regulating every aspect of RNA function. Thanks to the development of high-throughput sequencing technologies, transcriptome-wide profiling of RNA modifications has been made possible. With the accumulation of a large number of high-throughput datasets, bioinformatics approaches have become increasing critical for unraveling the epitranscriptome. We review here the recent progress in bioinformatics approaches for deciphering the epitranscriptomes, including epitranscriptome data analysis techniques, RNA modification databases, disease-association inference, general functional annotation, and studies on RNA modification site prediction. We also discuss the limitations of existing approaches and offer some future perspectives.
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Affiliation(s)
- Lian Liu
- School of Computer Sciences, Shannxi Normal University, Xi’an, Shaanxi 710119, China
| | - Bowen Song
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Jiani Ma
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Yi Song
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Yujiao Tang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Xiangyu Wu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Kunqi Chen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Jionglong Su
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
| | - Rong Rong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Zhiliang Lu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - João Pedro de Magalhães
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Shao-Wu Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Yufei Huang
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, 78249, USA
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiujuan Lei
- School of Computer Sciences, Shannxi Normal University, Xi’an, Shaanxi 710119, China
| | - Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
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22
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Wang T, Kong S, Tao M, Ju S. The potential role of RNA N6-methyladenosine in Cancer progression. Mol Cancer 2020; 19:88. [PMID: 32398132 PMCID: PMC7216508 DOI: 10.1186/s12943-020-01204-7] [Citation(s) in RCA: 533] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is considered the most common, abundant, and conserved internal transcript modification, especially in eukaryotic messenger RNA (mRNA). m6A is installed by m6A methyltransferases (METTL3/14, WTAP, RBM15/15B, VIRMA and ZC3H13, termed “writers”), removed by demethylases (FTO, ALKBH5, and ALKBH3, termed “erasers”), and recognized by m6A-binding proteins (YTHDC1/2, YTHDF1/2/3, IGF2BP1/2/3, HNRNP, and eIF3, termed “readers”). Accumulating evidence suggests that m6A RNA methylation greatly impacts RNA metabolism and is involved in the pathogenesis of many kinds of diseases, including cancers. In this review, we focus on the physiological functions of m6A modification and its related regulators, as well as on the potential biological roles of these elements in human tumors.
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Affiliation(s)
- Tianyi Wang
- 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, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shan Kong
- 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, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Mei Tao
- 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, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China. .,School of Public Health, Nantong University, NO 9, Seyuan Road, Nantong, 226019, Jiangsu, China.
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23
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Furlan M, Tanaka I, Leonardi T, de Pretis S, Pelizzola M. Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts. Front Genet 2020; 11:394. [PMID: 32425981 PMCID: PMC7212349 DOI: 10.3389/fgene.2020.00394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/30/2020] [Indexed: 01/24/2023] Open
Abstract
It has been known for a few decades that transcripts can be marked by dozens of different modifications. Yet, we are just at the beginning of charting these marks and understanding their functional impact. High-quality methods were developed for the profiling of some of these marks, and approaches to finely study their impact on specific phases of the RNA life-cycle are available, including RNA metabolic labeling. Thanks to these improvements, the most abundant marks, including N6-methyladenosine, are emerging as important determinants of the fate of marked RNAs. However, we still lack approaches to directly study how the set of marks for a given RNA molecule shape its fate. In this perspective, we first review current leading approaches in the field. Then, we propose an experimental and computational setup, based on direct RNA sequencing and mathematical modeling, to decipher the functional consequences of RNA modifications on the fate of individual RNA molecules and isoforms.
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Affiliation(s)
- Mattia Furlan
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
- Department of Physics, National Institute of Nuclear Physics, University of Turin, Turin, Italy
| | - Iris Tanaka
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tommaso Leonardi
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Stefano de Pretis
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
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24
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McIntyre ABR, Gokhale NS, Cerchietti L, Jaffrey SR, Horner SM, Mason CE. Limits in the detection of m 6A changes using MeRIP/m 6A-seq. Sci Rep 2020; 10:6590. [PMID: 32313079 PMCID: PMC7170965 DOI: 10.1038/s41598-020-63355-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Many cellular mRNAs contain the modified base m6A, and recent studies have suggested that various stimuli can lead to changes in m6A. The most common method to map m6A and to predict changes in m6A between conditions is methylated RNA immunoprecipitation sequencing (MeRIP-seq), through which methylated regions are detected as peaks in transcript coverage from immunoprecipitated RNA relative to input RNA. Here, we generated replicate controls and reanalyzed published MeRIP-seq data to estimate reproducibility across experiments. We found that m6A peak overlap in mRNAs varies from ~30 to 60% between studies, even in the same cell type. We then assessed statistical methods to detect changes in m6A peaks as distinct from changes in gene expression. However, from these published data sets, we detected few changes under most conditions and were unable to detect consistent changes across studies of similar stimuli. Overall, our work identifies limits to MeRIP-seq reproducibility in the detection both of peaks and of peak changes and proposes improved approaches for analysis of peak changes.
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Affiliation(s)
- Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, 10065, USA.
- Tri-Institutional Program in Computational Biology and Medicine, New York City, NY, 10065, USA.
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Leandro Cerchietti
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York City, NY, 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, New York City, NY, 10065, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, 10065, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA.
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25
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Baquero-Perez B, Antanaviciute A, Yonchev ID, Carr IM, Wilson SA, Whitehouse A. The Tudor SND1 protein is an m 6A RNA reader essential for replication of Kaposi's sarcoma-associated herpesvirus. eLife 2019; 8:e47261. [PMID: 31647415 PMCID: PMC6812964 DOI: 10.7554/elife.47261] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal RNA modification of cellular mRNAs. m6A is recognised by YTH domain-containing proteins, which selectively bind to m6A-decorated RNAs regulating their turnover and translation. Using an m6A-modified hairpin present in the Kaposi's sarcoma associated herpesvirus (KSHV) ORF50 RNA, we identified seven members from the 'Royal family' as putative m6A readers, including SND1. RIP-seq and eCLIP analysis characterised the SND1 binding profile transcriptome-wide, revealing SND1 as an m6A reader. We further demonstrate that the m6A modification of the ORF50 RNA is critical for SND1 binding, which in turn stabilises the ORF50 transcript. Importantly, SND1 depletion leads to inhibition of KSHV early gene expression showing that SND1 is essential for KSHV lytic replication. This work demonstrates that members of the 'Royal family' have m6A-reading ability, greatly increasing their epigenetic functions beyond protein methylation.
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Affiliation(s)
- Belinda Baquero-Perez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
- Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
| | - Agne Antanaviciute
- Leeds Institute of Medical Research, School of MedicineUniversity of Leeds, St James's University HospitalLeedsUnited Kingdom
| | - Ivaylo D Yonchev
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUnited Kingdom
- Sheffield Institute For Nucleic AcidsUniversity of SheffieldSheffieldUnited Kingdom
| | - Ian M Carr
- Leeds Institute of Medical Research, School of MedicineUniversity of Leeds, St James's University HospitalLeedsUnited Kingdom
| | - Stuart A Wilson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUnited Kingdom
- Sheffield Institute For Nucleic AcidsUniversity of SheffieldSheffieldUnited Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
- Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
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26
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Zhu W, Wang JZ, Xu Z, Cao M, Hu Q, Pan C, Guo M, Wei JF, Yang H. Detection of N6‑methyladenosine modification residues (Review). Int J Mol Med 2019; 43:2267-2278. [PMID: 31017262 PMCID: PMC6488182 DOI: 10.3892/ijmm.2019.4169] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
Among a number of mRNA modifications, N6‑methyladenosine (m6A) modification is the most common type in eukaryotes and nuclear‑replicating viruses. m6A has a significant role in numerous cancer types, including leukemia, brain tumors, liver cancer, breast cancer and lung cancer. Although m6A methyltransferases are essential during RNA modifications, the biological functions of m6A and the underlying mechanisms remain to be fully elucidated, predominantly due to the limited detection methods for m6A. In the present review, the currently available m6A detection methods and the respective scope of their applications are presented to facilitate the further investigation of the roles of m6A in biological process.
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Affiliation(s)
- Wei Zhu
- Research Division of Clinical Pharmacology
| | - Jing-Zi Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University
| | | | - Mengda Cao
- Research Division of Clinical Pharmacology
| | - Qiaoli Hu
- Research Division of Clinical Pharmacology
| | - Chen Pan
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 210000, P.R. China
| | - Miao Guo
- Research Division of Clinical Pharmacology
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University
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27
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Manners O, Baquero-Perez B, Whitehouse A. m 6A: Widespread regulatory control in virus replication. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:370-381. [PMID: 30412798 PMCID: PMC6414752 DOI: 10.1016/j.bbagrm.2018.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]
Abstract
N6-methyladenosine (m6A) is a highly pervasive and dynamic modification found on eukaryotic RNA. Despite the failure to comprehend the true regulatory potential of this epitranscriptomic mark for decades, our knowledge of m6A has rapidly expanded in recent years. The modification has now been functionally linked to all stages of mRNA metabolism and demonstrated to regulate a variety of biological processes. Furthermore, m6A has been identified on transcripts encoded by a wide range of viruses. Studies to investigate m6A function in viral-host interactions have highlighted distinct roles indicating widespread regulatory control over viral life cycles. As a result, unveiling the true influence of m6A modification could revolutionise our comprehension of the regulatory mechanisms controlling viral replication. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Oliver Manners
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Belinda Baquero-Perez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
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28
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Wang IX, Grunseich C, Fox J, Burdick J, Zhu Z, Ravazian N, Hafner M, Cheung VG. Human proteins that interact with RNA/DNA hybrids. Genome Res 2018; 28:1405-1414. [PMID: 30108179 PMCID: PMC6120628 DOI: 10.1101/gr.237362.118] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/27/2018] [Indexed: 12/16/2022]
Abstract
RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop. Knowledge of how they form and resolve, as well as their functional roles, is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions, including most steps of RNA processing. The proteins are enriched for K homology (KH) and helicase domains. Among them, more than 300 proteins preferred binding to hybrids than double-stranded DNA. These proteins serve as starting points for mechanistic studies to elucidate what RNA/DNA hybrids regulate and how they are regulated.
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Affiliation(s)
- Isabel X Wang
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland 20892, USA
| | - Jennifer Fox
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Joshua Burdick
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Niema Ravazian
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892, USA
| | - Vivian G Cheung
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
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29
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Chen X, Sun YZ, Liu H, Zhang L, Li JQ, Meng J. RNA methylation and diseases: experimental results, databases, Web servers and computational models. Brief Bioinform 2017; 20:896-917. [DOI: 10.1093/bib/bbx142] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/12/2017] [Indexed: 12/15/2022] Open
Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University
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