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XIONG J, FENG T, YUAN BF. [Advances in mapping analysis of ribonucleic acid modifications through sequencing]. Se Pu 2024; 42:632-645. [PMID: 38966972 PMCID: PMC11224946 DOI: 10.3724/sp.j.1123.2023.12025] [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: 12/20/2023] [Indexed: 07/06/2024] Open
Abstract
Over 170 chemical modifications have been discovered in various types of ribonucleic acids (RNAs), including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). These RNA modifications play crucial roles in a wide range of biological processes such as gene expression regulation, RNA stability maintenance, and protein translation. RNA modifications represent a new dimension of gene expression regulation known as the "epitranscriptome". The discovery of RNA modifications and the relevant writers, erasers, and readers provides an important basis for studies on the dynamic regulation and physiological functions of RNA modifications. Owing to the development of detection technologies for RNA modifications, studies on RNA epitranscriptomes have progressed to the single-base resolution, multilayer, and full-coverage stage. Transcriptome-wide methods help discover new RNA modification sites and are of great importance for elucidating the molecular regulatory mechanisms of epitranscriptomics, exploring the disease associations of RNA modifications, and understanding their clinical applications. The existing RNA modification sequencing technologies can be categorized according to the pretreatment approach and sequencing principle as direct high-throughput sequencing, antibody-enrichment sequencing, enzyme-assisted sequencing, chemical labeling-assisted sequencing, metabolic labeling sequencing, and nanopore sequencing technologies. These methods, as well as studies on the functions of RNA modifications, have greatly expanded our understanding of epitranscriptomics. In this review, we summarize the recent progress in RNA modification detection technologies, focusing on the basic principles, advantages, and limitations of different methods. Direct high-throughput sequencing methods do not require complex RNA pretreatment and allow for the mapping of RNA modifications using conventional RNA sequencing methods. However, only a few RNA modifications can be analyzed by high-throughput sequencing. Antibody enrichment followed by high-throughput sequencing has emerged as a crucial approach for mapping RNA modifications, significantly advancing the understanding of RNA modifications and their regulatory functions in different species. However, the resolution of antibody-enrichment sequencing is limited to approximately 100-200 bp. Although chemical crosslinking techniques can achieve single-base resolution, these methods are often complex, and the specificity of the antibodies used in these methods has raised concerns. In particular, the issue of off-target binding by the antibodies requires urgent attention. Enzyme-assisted sequencing has improved the accuracy of the localization analysis of RNA modifications and enables stoichiometric detection with single-base resolution. However, the enzymes used in this technique show poor reactivity, specificity, and sequence preference. Chemical labeling sequencing has become a widely used approach for profiling RNA modifications, particularly by altering reverse transcription (RT) signatures such as RT stops, misincorporations, and deletions. Chemical-assisted sequencing provides a sequence-independent RNA modification detection strategy that enables the localization of multiple RNA modifications. Additionally, when combined with the biotin-streptavidin affinity method, low-abundance RNA modifications can be enriched and detected. Nevertheless, the specificity of many chemical reactions remains problematic, and the development of specific reaction probes for particular modifications should continue in the future to achieve the precise localization of RNA modifications. As an indirect localization method, metabolic labeling sequencing specifically localizes the sites at which modifying enzymes act, which is of great significance in the study of RNA modification functions. However, this method is limited by the intracellular labeling of RNA and cannot be applied to biological samples such as clinical tissues and blood samples. Nanopore sequencing is a direct RNA-sequencing method that does not require RT or the polymerase chain reaction (PCR). However, challenges in analyzing the data obtained from nanopore sequencing, such as the high rate of false positives, must be resolved. Discussing sequencing analysis methods for various types of RNA modifications is instructive for the future development of novel RNA modification mapping technologies, and will aid studies on the functions of RNA modifications across the entire transcriptome.
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Li Y, Yi Y, Gao X, Wang X, Zhao D, Wang R, Zhang LS, Gao B, Zhang Y, Zhang L, Cao Q, Chen K. 2'-O-methylation at internal sites on mRNA promotes mRNA stability. Mol Cell 2024; 84:2320-2336.e6. [PMID: 38906115 PMCID: PMC11196006 DOI: 10.1016/j.molcel.2024.04.011] [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: 10/24/2022] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/23/2024]
Abstract
2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yang Yi
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Wang
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yadong Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA; Prostate Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
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3
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Zhou KI, Pecot CV, Holley CL. 2'- O-methylation (Nm) in RNA: progress, challenges, and future directions. RNA (NEW YORK, N.Y.) 2024; 30:570-582. [PMID: 38531653 PMCID: PMC11019748 DOI: 10.1261/rna.079970.124] [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: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
RNA 2'-O-methylation (Nm) is highly abundant in noncoding RNAs including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), and occurs in the 5' cap of virtually all messenger RNAs (mRNAs) in higher eukaryotes. More recently, Nm has also been reported to occur at internal sites in mRNA. High-throughput methods have been developed for the transcriptome-wide detection of Nm. However, these methods have mostly been applied to abundant RNAs such as rRNA, and the validity of the internal mRNA Nm sites detected with these approaches remains controversial. Nonetheless, Nm in both coding and noncoding RNAs has been demonstrated to impact cellular processes, including translation and splicing. In addition, Nm modifications at the 5' cap and possibly at internal sites in mRNA serve to prevent the binding of nucleic acid sensors, thus preventing the activation of the innate immune response by self-mRNAs. Finally, Nm has been implicated in a variety of diseases including cancer, cardiovascular diseases, and neurologic syndromes. In this review, we discuss current challenges in determining the distribution, regulation, function, and disease relevance of Nm, as well as potential future directions for the field.
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Affiliation(s)
- Katherine I Zhou
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- University of North Carolina RNA Discovery Center, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christopher L Holley
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
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4
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Tang Y, Wu Y, Wang S, Lu X, Gu X, Li Y, Yang F, Xu R, Wang T, Jiao Z, Wu Y, Liu L, Chen JQ, Wang Q, Chen Q. An integrative platform for detection of RNA 2'-O-methylation reveals its broad distribution on mRNA. CELL REPORTS METHODS 2024; 4:100721. [PMID: 38452769 PMCID: PMC10985248 DOI: 10.1016/j.crmeth.2024.100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/29/2023] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
Ribose 2'-O-methylation is involved in critical biological processes, but its biological functions and significance in mRNAs remain underexplored. We have developed NJU-seq, a sensitive method for unbiased 2'-O-methylation (Nm) profiling, and Nm-VAQ, a site-specific quantification tool. Using these tools in tandem, we identified thousands of Nm sites on mRNAs of human and mouse cell lines, of which 68 of 84 selected sites were further validated to be more than 1% 2'-O-methylated. Unlike rRNA, most mRNA Nm sites were from 1% to 30% methylated. In addition, mRNA Nm was dynamic, changing according to the circumstance. Furthermore, we show that fibrillarin is involved as a methyltransferase. By mimicking the detected Nm sites and the context sequence, the RNA fragments could be 2'-O-methylated and demonstrated higher stability but lower translation efficiency. Last, profiling of Nm sites in lung surgery samples revealed common signatures of lung cancer pathogenesis, providing potential new diagnostic markers.
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Affiliation(s)
- Yao Tang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China; Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Yifan Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Sainan Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaolan Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China; Department of Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Xiangwen Gu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yong Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Fan Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ruilin Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Tao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Zichen Jiao
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Liwei Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jian-Qun Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Qiang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Qihan Chen
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.
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Zhang LS, Ye C, Ju CW, Gao B, Feng X, Sun HL, Wei J, Yang F, Dai Q, He C. BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution. Nat Protoc 2024; 19:517-538. [PMID: 37968414 PMCID: PMC11007761 DOI: 10.1038/s41596-023-00917-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 09/25/2023] [Indexed: 11/17/2023]
Abstract
Pseudouridine (Ψ) is an abundant RNA modification that is present in and affects the functions of diverse non-coding RNA species, including rRNA, tRNA and small nuclear RNA. Ψ also exists in mammalian mRNA and probably exhibits functional roles; however, functional investigations of mRNA Ψ modifications in mammals have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed bisulfite-induced deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol for mapping Ψ distribution across cellular mRNAs, which includes fast steps in both library preparation and data analysis. This protocol generates highly reproducible results by inducing high deletion ratios at Ψ modification within diverse sequence contexts, and meanwhile displayed almost zero background deletions at unmodified uridines. When used for transcriptome-wide Ψ profiling in mouse embryonic stem cells, the current protocol uncovered 8,407 Ψ sites from as little as 10 ng of polyA+ RNA input. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS) and data analysis. Library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe ( https://github.com/y9c/pseudoU-BIDseq ), a user-friendly data analysis pipeline for Ψ site detection and modification stoichiometry quantification, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from BID-seq data.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Cheng-Wei Ju
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xinran Feng
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Hui-Lung Sun
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Fan Yang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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6
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Zhang LS, Dai Q, He C. Base-Resolution Sequencing Methods for Whole-Transcriptome Quantification of mRNA Modifications. Acc Chem Res 2024; 57:47-58. [PMID: 38079380 PMCID: PMC10765377 DOI: 10.1021/acs.accounts.3c00532] [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: 08/30/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
RNA molecules are not merely a combination of four bases of A, C, G, and U. Chemical modifications occur in almost all RNA species and play diverse roles in gene expression regulation. The abundant cellular RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), are known to have the highest density of RNA modifications, which exert critical functions in rRNA and tRNA biogenesis, stability, and subsequent translation. In recent years, modifications on low-abundance RNA species in mammalian cells, such as messenger RNA (mRNA), regulatory noncoding RNA (ncRNA), and chromatin-associated RNA (caRNA), have been shown to contain multiple different chemical modifications with functional significance. As the most abundant mRNA modification in mammals, N6-methyladenosine (m6A) affects nearly every stage of mRNA processing and metabolism, with the antibody-based m6A-MeRIP-seq (methylated RNA immunoprecipitation sequencing) followed by high-throughput sequencing widely employed in mapping m6A distribution transcriptome-wide in diverse biological systems. In addition to m6A, other chemical modifications such as pseudouridine (Ψ), 2'-O-methylation (Nm), 5-methylcytidine (m5C), internal N7-methylguanosine (m7G), N1-methyladenosine (m1A), N4-acetylcytidine (ac4C), etc. also exist in polyA-tailed RNA in mammalian cells, requiring effective mapping approaches for whole-transcriptome profiling of these non-m6A mRNA modifications. Like m6A, the antibody-based enrichment followed by sequencing has been the primary method to study distributions of these modifications. Methods to more quantitatively map these modifications would dramatically improve our understanding of distributions and modification density of these chemical marks on RNA, thereby bettering informing functional implications. In this Account, aimed at both single-base resolution and modification fraction quantification, we summarize our recent advances in developing a series of chemistry- or biochemistry-based methods to quantitatively map RNA modifications, including m6A, Ψ, m5C, m1A, 2'-O-methylation (Nm), and internal m7G, in mammalian mRNA at base resolution. These new methods, including m6A-SAC-seq, eTAM-seq, BID-seq, UBS-seq, DAMM-seq, m1A-quant-seq, Nm-Mut-seq, and m7G-quant-seq, promise to conduct base-resolution mapping of most major mRNA modifications with low RNA input and uncover dynamic changes in modification stoichiometry during biological and physiological processes, facilitating future investigations on these RNA modifications in regulating cellular gene expression and as potential biomarkers for clinical diagnosis and prognosis. These quantitative sequencing methods allow the mapping of most mRNA modifications with limited input sample requirements. The same modifications on diverse RNA species, such as caRNA, ncRNA, nuclear nascent RNA, mitochondrial RNA, cell-free RNA (cfRNA), etc., could be sequenced using the same methods.
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Affiliation(s)
- Li-Sheng Zhang
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, The Hong Kong University of
Science and Technology (HKUST), Kowloon 999077, Hong
Kong SAR, China
- Division
of Life Science, The Hong Kong University
of Science and Technology (HKUST), Kowloon 999077, Hong
Kong SAR, China
| | - Qing Dai
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
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7
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Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [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: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
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Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
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Zhang LS, Ju CW, Jiang B, He C. Base-resolution quantitative DAMM-seq for mapping RNA methylations in tRNA and mitochondrial polycistronic RNA. Methods Enzymol 2023; 692:39-54. [PMID: 37925186 PMCID: PMC10882886 DOI: 10.1016/bs.mie.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
The human AlkB family proteins, such as FTO and ALKBH5, are known to mediate RNA m6A demethylation. However, although ALKBH7 localizes in mitochondria and affects metabolism, the detailed biological function and mechanism have remained unknown for years. We developed Demethylation-Assisted Multiple Methylation sequencing (DAMM-seq) to simultaneously detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) methylations in both steady-state RNA and nascent RNA, and discovered that human ALKBH7 demethylates m22G and m1A within mt-Ile and mt-Leu1 pre-tRNA regions, respectively, in mitochondrial polycistronic RNA. DAMM-seq quantitatively and sensitively monitors the methylation stoichiometry change at pre-tRNA junctions within nascent mt-RNA, revealing the target region where ALKBH7 regulates RNA processing and local structural switch of polycistronic mt-RNAs. A new RNA demethylase in human cells was characterized through the base-resolution quantification of multiple RNA methylations in nascent mt-RNA, resolving the long-standing question about the functional substrate of ALKBH7.
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Affiliation(s)
- Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Hong Kong SAR, P.R. China; Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Hong Kong SAR, P.R. China; Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States.
| | - Cheng-Wei Ju
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | - Bochen Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
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