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Yang Y, Nakayama K, Okada S, Sato K, Wada T, Sakaguchi Y, Murayama A, Suzuki T, Sakurai M. ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification. FEBS Lett 2024; 598:1080-1093. [PMID: 38523059 DOI: 10.1002/1873-3468.14854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.
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Affiliation(s)
- Yuxi Yang
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Koki Nakayama
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, Izumo-shi, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Ayaka Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Masayuki Sakurai
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
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2
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Quillin AL, Arnould B, Knutson SD, Heemstra JM. Spatial visualization of A-to-I Editing in cells using Endonuclease V Immunostaining Assay (EndoVIA). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583344. [PMID: 38496620 PMCID: PMC10942280 DOI: 10.1101/2024.03.04.583344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Adenosine-to-Inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited. Current methods rely primarily on in vitro characterization of extracted RNA that ultimately erases subcellular localization and cell-to-cell heterogeneity. To address these challenges, we have repurposed Endonuclease V (EndoV), a magnesium dependent ribonuclease that cleaves inosine bases in edited RNA, to selectively bind and detect A-to-I edited RNA in cells. The work herein introduces Endonuclease V Immunostaining Assay (EndoVIA), a workflow that provides spatial visualization of edited transcripts, enables rapid quantification of overall inosine abundance, and maps the landscape of A-to-I editing within the transcriptome at the nanoscopic level.
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3
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Kaur R, Wetmore SD. Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. J Chem Inf Model 2024; 64:944-959. [PMID: 38253321 DOI: 10.1021/acs.jcim.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. In silico K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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4
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Xu Y, Liu J, Zhao T, Song F, Tian L, Cai W, Li H, Duan Y. Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes. Int J Mol Sci 2023; 24:17126. [PMID: 38138955 PMCID: PMC10742984 DOI: 10.3390/ijms242417126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuange Duan
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.X.); (J.L.); (T.Z.); (F.S.); (L.T.); (W.C.); (H.L.)
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5
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Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023; 56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by the adenosine deaminase acting on the RNA (ADAR) family of enzymes of which there are three members (ADAR1, ADAR2, and ADAR3), is a major gene regulatory mechanism that diversifies the transcriptome. It is widespread in many metazoans, including humans. As inosine is interpreted by cellular machineries mainly as guanosine, A-to-I editing effectively gives A-to-G nucleotide changes. Depending on its location, an editing event can generate new protein isoforms or influence other RNA processing pathways. Researchers have found that ADAR-mediated editing performs diverse functions. For example, it enables living organisms such as cephalopods to adapt rapidly to fluctuating environmental conditions such as water temperature. In development, the loss of ADAR1 is embryonically lethal partly because endogenous double-stranded RNAs (dsRNAs) are no longer marked by inosines, which signal "self", and thus cause the melanoma differentiation-associated protein 5 (MDA5) sensor to trigger a deleterious interferon response. Hence, ADAR1 plays a key role in preventing aberrant activation of the innate immune system. Furthermore, ADAR enzymes have been implicated in myriad human diseases. Intriguingly, some cancer cells are known to exploit ADAR1 activity to dodge immune responses. However, the exact identities of immunogenic RNAs in different biological contexts have remained elusive. Consequently, there is tremendous interest in identifying inosine-containing RNAs in the cell.The identification of A-to-I RNA editing sites is dependent on the sequencing of nucleic acids. Technological and algorithmic advancements over the past decades have revolutionized the way editing events are detected. At the beginning, the discovery of editing sites relies on Sanger sequencing, a first-generation technology. Both RNA, which is reverse transcribed into complementary DNA (cDNA), and genomic DNA (gDNA) from the same source are analyzed. After sequence alignment, one would require an adenosine to be present in the genome but a guanosine to be detected in the RNA sample for a position to be declared as an editing site. However, an issue with Sanger sequencing is its low throughput. Subsequently, Illumina sequencing, a second-generation technology, was invented. By permitting the simultaneous interrogation of millions of molecules, it enables many editing sites to be identified rapidly. However, a key challenge is that the Illumina platform produces short sequencing reads that can be difficult to map accurately. To tackle the challenge, we and others developed computational workflows with a series of filters to discard sites that are likely to be false positives. When Illumina sequencing data sets are properly analyzed, A-to-G variants should emerge as the most dominant mismatch type. Moreover, the quantitative nature of the data allows us to build a comprehensive atlas of editing-level measurements across different biological contexts, providing deep insights into the spatiotemporal dynamics of RNA editing. However, difficulties remain in identifying true A-to-I editing sites in short protein-coding exons or in organisms and diseases where DNA mutations and genomic polymorphisms are prevalent and mostly unknown. Nanopore sequencing, a third-generation technology, promises to address the difficulties, as it allows native RNAs to be sequenced without conversion to cDNA, preserving base modifications that can be directly detected through machine learning. We recently demonstrated that nanopore sequencing could be used to identify A-to-I editing sites in native RNA directly. Although further work is needed to enhance the detection accuracy in single molecules from fewer cells, the nanopore technology holds the potential to revolutionize epitranscriptomic studies.
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Affiliation(s)
- Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- HP-NTU Digital Manufacturing Corporate Laboratory, Nanyang Technological University, Singapore 637460, Singapore
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6
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Sun H, Li K, Liu C, Yi C. Regulation and functions of non-m 6A mRNA modifications. Nat Rev Mol Cell Biol 2023; 24:714-731. [PMID: 37369853 DOI: 10.1038/s41580-023-00622-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Nucleobase modifications are prevalent in eukaryotic mRNA and their discovery has resulted in the emergence of epitranscriptomics as a research field. The most abundant internal (non-cap) mRNA modification is N6-methyladenosine (m6A), the study of which has revolutionized our understanding of post-transcriptional gene regulation. In addition, numerous other mRNA modifications are gaining great attention because of their major roles in RNA metabolism, immunity, development and disease. In this Review, we focus on the regulation and function of non-m6A modifications in eukaryotic mRNA, including pseudouridine (Ψ), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), inosine, 5-methylcytidine (m5C), N4-acetylcytidine (ac4C), 2'-O-methylated nucleotide (Nm) and internal N7-methylguanosine (m7G). We highlight their regulation, distribution, stoichiometry and known roles in mRNA metabolism, such as mRNA stability, translation, splicing and export. We also discuss their biological consequences in physiological and pathological processes. In addition, we cover research techniques to further study the non-m6A mRNA modifications and discuss their potential future applications.
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Affiliation(s)
- Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Kai Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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7
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Staitieh BS, Hu X, Yeligar SM, Auld SC. Paired ATAC- and RNA-seq offer insight into the impact of HIV on alveolar macrophages: a pilot study. Sci Rep 2023; 13:15276. [PMID: 37714998 PMCID: PMC10504379 DOI: 10.1038/s41598-023-42644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023] Open
Abstract
People with HIV remain at greater risk for both infectious and non-infectious pulmonary diseases even after antiretroviral therapy initiation and CD4 cell count recovery. These clinical risks reflect persistent HIV-mediated defects in innate and adaptive immunity, including in the alveolar macrophage, a key innate immune effector in the lungs. In this proof-of-concept pilot study, we leveraged paired RNA-seq and ATAC-seq analyses of human alveolar macrophages obtained with research bronchoscopy from people with and without HIV to highlight the potential for recent methodologic advances to generate novel hypotheses about biological pathways that may contribute to impaired pulmonary immune function in people with HIV. In addition to 35 genes that were differentially expressed in macrophages from people with HIV, gene set enrichment analysis identified six gene sets that were differentially regulated. ATAC-seq analysis revealed 115 genes that were differentially accessible for people with HIV. Data-driven integration of the findings from these complementary, high-throughput techniques using xMWAS identified distinct clusters involving lipoprotein lipase and inflammatory pathways. By bringing together transcriptional and epigenetic data, this analytic approach points to several mechanisms, including previously unreported pathways, that warrant further exploration as potential mediators of the increased risk of pulmonary disease in people with HIV.
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Affiliation(s)
- Bashar S Staitieh
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA
- Grady Health System, Atlanta, GA, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Samantha M Yeligar
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA
- Veterans Affairs Atlanta Healthcare System, Decatur, GA, USA
| | - Sara C Auld
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA.
- Departments of Epidemiology and Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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8
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Wei Q, Han S, Yuan K, He Z, Chen Y, Xi X, Han J, Yan S, Chen Y, Yuan B, Weng X, Zhou X. Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq. Nucleic Acids Res 2023; 51:e87. [PMID: 37470992 PMCID: PMC10484733 DOI: 10.1093/nar/gkad604] [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: 01/28/2023] [Revised: 06/23/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional processing event involved in diversifying the transcriptome and is responsible for various biological processes. In this context, we developed a new method based on the highly selective cleavage activity of Endonuclease V against Inosine and the universal activity of sodium periodate against all RNAs to enrich the inosine-containing RNA and accurately identify the editing sites. We validated the reliability of our method in human brain in both Alu and non-Alu elements. The conserved sites of A-to-I editing in human cells (HEK293T, HeLa, HepG2, K562 and MCF-7) primarily occurs in the 3'UTR of the RNA, which are highly correlated with RNA binding and protein binding. Analysis of the editing sites between the human brain and mouse brain revealed that the editing of exons is more conserved than that in other regions. This method was applied to three neurological diseases (Alzheimer's, epilepsy and ageing) of mouse brain, reflecting that A-to-I editing sites significantly decreased in neuronal activity genes.
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Affiliation(s)
- Qi Wei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Kexin Yuan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Xin Xi
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Jingyu Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Shen Yan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Bifeng Yuan
- School of Public Health, Wuhan University, Wuhan, HuBei 430071, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, PR China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
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9
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Li K, Peng J, Yi C. Sequencing methods and functional decoding of mRNA modifications. FUNDAMENTAL RESEARCH 2023; 3:738-748. [PMID: 38933299 PMCID: PMC11197720 DOI: 10.1016/j.fmre.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/27/2023] [Accepted: 05/07/2023] [Indexed: 06/28/2024] Open
Abstract
More than 160 types of post-transcriptional RNA modifications have been reported; there is substantial variation in modification type, abundance, site, and function across species, tissues, and RNA type. The recent development of high-throughput detection technology has enabled identification of diverse dynamic and reversible RNA modifications, including N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). In this review, we focus on eukaryotic mRNA modifications. We summarize their biogenesis, regulatory mechanisms, and biological functions, as well as high-throughput methods for detection of mRNA modifications. We also discuss challenges that must be addressed in mRNA modification research.
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Affiliation(s)
- Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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10
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Liu C, Sun H, Yi Y, Shen W, Li K, Xiao Y, Li F, Li Y, Hou Y, Lu B, Liu W, Meng H, Peng J, Yi C, Wang J. Absolute quantification of single-base m 6A methylation in the mammalian transcriptome using GLORI. Nat Biotechnol 2023; 41:355-366. [PMID: 36302990 DOI: 10.1038/s41587-022-01487-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/24/2022] [Indexed: 12/22/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian cells and the best-studied epitranscriptomic mark. Despite the development of various tools to map m6A, a transcriptome-wide method that enables absolute quantification of m6A at single-base resolution is lacking. Here we use glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI) to develop an absolute m6A quantification method that is conceptually similar to bisulfite-sequencing-based quantification of DNA 5-methylcytosine. We apply GLORI to quantify the m6A methylomes of mouse and human cells and reveal clustered m6A modifications with differential distribution and stoichiometry. In addition, we characterize m6A dynamics under stress and examine the quantitative landscape of m6A modification in gene expression regulation. GLORI is an unbiased, convenient method for the absolute quantification of the m6A methylome.
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Affiliation(s)
- Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yunpeng Yi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan, China
| | - Weiguo Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Kai Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Ye Xiao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fei Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yuchen Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yongkang Hou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Wenqing Liu
- School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
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11
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Swenson C, Argueta-Gonzalez HS, Sterling SA, Robichaux R, Knutson SD, Heemstra JM. Forced Intercalation Peptide Nucleic Acid Probes for the Detection of an Adenosine-to-Inosine Modification. ACS OMEGA 2023; 8:238-248. [PMID: 36643573 PMCID: PMC9835161 DOI: 10.1021/acsomega.2c03568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The deamination of adenosine to inosine is an important modification in nucleic acids that functionally recodes the identity of the nucleobase to a guanosine. Current methods to analyze and detect this single nucleotide change, such as sequencing and PCR, typically require time-consuming or costly procedures. Alternatively, fluorescent "turn-on" probes that result in signal enhancement in the presence of target are useful tools for real-time detection and monitoring of nucleic acid modification. Here we describe forced-intercalation PNA (FIT-PNA) probes that are designed to bind to inosine-containing nucleic acids and use thiazole orange (TO), 4-dimethylamino-naphthalimide (4DMN), and malachite green (MG) fluorogenic dyes to detect A-to-I editing events. We show that incorporation of the dye as a surrogate base negatively affects the duplex stability but does not abolish binding to targets. We then determined that the identity of the adjacent nucleobase and temperature affect the overall signal and fluorescence enhancement in the presence of inosine, achieving an 11-fold increase, with a limit of detection (LOD) of 30 pM. We determine that TO and 4DMN probes are viable candidates to enable selective inosine detection for biological applications.
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Affiliation(s)
- Colin
S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | - Sierra A. Sterling
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ryan Robichaux
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Steve D. Knutson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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12
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Kaur R, Aboelnga MM, Nikkel DJ, Wetmore SD. The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme. Phys Chem Chem Phys 2022; 24:29130-29140. [PMID: 36444615 DOI: 10.1039/d2cp04338f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the one-metal mediated pathway is debated. Furthermore, one-metal mediated nucleases maintain activity in the presence of many different metals, but the underlying reasons for this broad metal specificity are unknown. The human apurinic/apyrimidinic endonuclease (APE1), which plays a key role in DNA repair, transcription regulation, and gene expression, is a prototypical example of a one-metal dependent nuclease. Although Mg2+ is the native metal cofactor, APE1 remains catalytically active in the presence of several metals, with the rate decreasing as Mg2+ > Mn2+ > Ni2+ > Zn2+, while Ca2+ completely abolished the activity. The present work uses quantum mechanics-molecular mechanics techniques to map APE1-facilitated phosphodiester bond hydrolysis in the presence of these metals. The structural differences in stationary points along the reaction pathway shed light on the interplay between several factors that allow APE1 to remain catalytically active for various metals, with the trend in the barrier heights correlating with the experimentally reported APE1 catalytic activity. In contrast, Ca2+ significantly changes the metal coordination and active site geometry, and thus completely inhibits catalysis. Our work thereby provides support for the controversial single-metal mediated phosphodiester bond cleavage and clarifies uncertainties regarding the role of the metal and metal identity in this important reaction. This information is key for future medicinal and biotechnological applications including disease diagnosis and treatment, and protein engineering.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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13
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Detection technologies for RNA modifications. Exp Mol Med 2022; 54:1601-1616. [PMID: 36266445 PMCID: PMC9636272 DOI: 10.1038/s12276-022-00821-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
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14
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Nowacka M, Latoch P, Izert MA, Karolak NK, Tomecki R, Koper M, Tudek A, Starosta AL, Górna M. A cap 0-dependent mRNA capture method to analyze the yeast transcriptome. Nucleic Acids Res 2022; 50:e132. [PMID: 36259646 PMCID: PMC9825183 DOI: 10.1093/nar/gkac903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 01/29/2023] Open
Abstract
Analysis of the protein coding transcriptome by the RNA sequencing requires either enrichment of the desired fraction of coding transcripts or depletion of the abundant non-coding fraction consisting mainly of rRNA. We propose an alternative mRNA enrichment strategy based on the RNA-binding properties of the human IFIT1, an antiviral protein recognizing cap 0 RNA. Here, we compare for Saccharomyces cerevisiae an IFIT1-based mRNA pull-down with yeast targeted rRNA depletion by the RiboMinus method. IFIT1-based RNA capture depletes rRNA more effectively, producing high quality RNA-seq data with an excellent coverage of the protein coding transcriptome, while depleting cap-less transcripts such as mitochondrial or some non-coding RNAs. We propose IFIT1 as a cost effective and versatile tool to prepare mRNA libraries for a variety of organisms with cap 0 mRNA ends, including diverse plants, fungi and eukaryotic microbes.
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Affiliation(s)
| | | | - Matylda A Izert
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Warsaw 02-093, Poland
| | - Natalia K Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Warsaw 02-093, Poland,Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Warsaw 02-093, Poland
| | - Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Warsaw 02-106, Poland,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Warsaw 02-106, Poland
| | - Michał Koper
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Warsaw 02-106, Poland
| | - Agnieszka Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Warsaw 02-106, Poland
| | - Agata L Starosta
- Correspondence may also be addressed to Agata L. Starosta. Tel: +48 22 592 33 41;
| | - Maria W Górna
- To whom correspondence should be addressed. Tel: +48 22 55 26 685;
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15
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Felix AS, Quillin AL, Mousavi S, Heemstra JM. Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications. Acc Chem Res 2022; 55:2271-2279. [PMID: 35900335 PMCID: PMC9388579 DOI: 10.1021/acs.accounts.2c00287] [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] [Indexed: 01/19/2023]
Abstract
RNA editing or "epitranscriptomic modification" refers to the processing of RNA that occurs after transcription to alter the sequence or structure of the nucleic acid. These chemical alterations can be found on either the ribose sugar or the nucleobase, and although many are "silent" and do not change the Watson-Crick-Franklin code of the RNA, others result in recoding events. More than 170 RNA modifications have been identified so far, each having a specific biological purpose. Additionally, dysregulated RNA editing has been linked to several types of diseases and disorders. As new modifications are discovered and our understanding of their functional impact grows, so does the need for selective methods of identifying and mapping editing sites in the transcriptome.The most common methods for studying RNA modifications rely on antibodies as affinity reagents; however, antibodies can be difficult to generate and often have undesirable off-target binding. More recently, selective chemical labeling has advanced the field by offering techniques that can be used for the detection, enrichment, and quantification of RNA modifications. In our method using acrylamide for inosine labeling, we demonstrated the versatility with which this approach enables pull-down or downstream functionalization with other tags or affinity handles. Although this method did enable the quantitative analysis of A-to-I editing levels, we found that selectivity posed a significant limitation, likely because of the similar reactivity profiles of inosine and pseudouridine or other nucleobases.Seeking to overcome the inherent limitations of antibodies and chemical labeling methods, a more recent approach to studying the epitranscriptome is through the repurposing of proteins and enzymes that recognize modified RNA. Our laboratory has used Endonuclease V, a repair enzyme that cleaves inosine-containing RNAs, and reprogrammed it to instead bind inosine. We first harnessed EndoV to develop a preparative technique for RNA sequencing that we termed EndoVIPER-seq. This method uses EndoV to enrich inosine-edited RNAs, providing better coverage in RNA sequencing and leading to the discovery of previously undetected A-to-I editing sites. We also leveraged EndoV to create a plate-based immunoassay (EndoVLISA) to quantify inosine in cellular RNA. This approach can detect differential A-to-I editing levels across tissue types or disease states while being independent of RNA sequencing, making it cost-effective and high-throughput. By harnessing the molecular recognition capabilities of this enzyme, we show that EndoV can be repurposed as an "anti-inosine antibody" to develop new methods of detecting and enriching inosine from cellular RNA.Nature has evolved a plethora of proteins and enzymes that selectively recognize and act on RNA modifications, and exploiting the affinity of these biomolecules offers a promising new direction for the field of epitranscriptomics.
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Affiliation(s)
- Ansley S. Felix
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Alexandria L. Quillin
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Shikufa Mousavi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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16
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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17
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Wang Y, Zhang X, Liu H, Zhou X. Chemical methods and advanced sequencing technologies for deciphering mRNA modifications. Chem Soc Rev 2021; 50:13481-13497. [PMID: 34792050 DOI: 10.1039/d1cs00920f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
RNA modification, like other epigenetic modifications such as DNA modification and histone modification, is an emerging player in the field of the posttranscriptional regulation of gene expression. More than 160 kinds of RNA modifications have been identified, and they are widely distributed in different types of RNA. Recently, researchers have increasingly used advanced technologies to study modified nucleic acids in order to elucidate their biological functions and expand the understanding of the central laws of epigenetics. In this tutorial review, we comprehensively outline current advanced techniques for decoding RNA modifications, highlighting some of the bottlenecks in existing approaches as well as new opportunities that may lead to innovations. With this review, we expect to provide chemistry and biology students and researchers with ideas for solving some challenging problems, such as how to simultaneously detect multiple types of modifications within the same system. Moreover, some low-coverage modifications that may act as 'candidates' in important transcriptional processes need to be further explored. These novel approaches have the potential to lay a foundation for understanding the nuanced complexities of the biological functions of RNA modification.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
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18
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Owens MC, Zhang C, Liu KF. Recent technical advances in the study of nucleic acid modifications. Mol Cell 2021; 81:4116-4136. [PMID: 34480848 DOI: 10.1016/j.molcel.2021.07.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/30/2022]
Abstract
Enzyme-mediated chemical modifications of nucleic acids are indispensable regulators of gene expression. Our understanding of the biochemistry and biological significance of these modifications has largely been driven by an ever-evolving landscape of technologies that enable accurate detection, mapping, and manipulation of these marks. Here we provide a summary of recent technical advances in the study of nucleic acid modifications with a focus on techniques that allow accurate detection and mapping of these modifications. For each modification discussed (N6-methyladenosine, 5-methylcytidine, inosine, pseudouridine, and N4-acetylcytidine), we begin by introducing the "gold standard" technique for its mapping and detection, followed by a discussion of techniques developed to address any shortcomings of the gold standard. By highlighting the commonalities and differences of these techniques, we hope to provide a perspective on the current state of the field and to lay out a guideline for development of future technologies.
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Affiliation(s)
- Michael C Owens
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Celia Zhang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Knutson SD, Heemstra JM. Protein-based molecular recognition tools for detecting and profiling RNA modifications. Curr Opin Struct Biol 2021; 69:1-10. [PMID: 33445115 PMCID: PMC8272725 DOI: 10.1016/j.sbi.2020.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/18/2022]
Abstract
RNA undergoes extensive biochemical modification following transcription. In addition to RNA splicing, transcripts are processed by a suite of enzymes that alter the chemical structure of different nucleobases. Broadly termed as 'RNA editing,' these modifications impart significant functional changes to translation, localization, and stability of individual transcripts within the cell. These changes are dynamic and required for a number of critical cellular processes, and dysregulation of these pathways is responsible for several disease states. Accurately detecting, measuring, and mapping different RNA modifications across the transcriptome is vital to understanding their broader functions as well as leveraging these events as diagnostic biomarkers. Here, we review recent advances in profiling several types of RNA modifications, with particular emphasis on adenosine-to-inosine (A-to-I) and N6-methyladenosine (m6A) RNA editing. We especially highlight approaches that utilize proteins to detect or enrich modified RNA transcripts before sequencing, and we summarize recent insights yielded from these techniques.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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20
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Knutson SD, Arthur RA, Johnston HR, Heemstra JM. Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay. Angew Chem Int Ed Engl 2021; 60:17009-17017. [PMID: 33979483 PMCID: PMC8562906 DOI: 10.1002/anie.202102762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing is a conserved eukaryotic RNA modification that contributes to development, immune response, and overall cellular function. Here, we utilize Endonuclease V (EndoV), which binds specifically to inosine in RNA, to develop an EndoV-linked immunosorbency assay (EndoVLISA) as a rapid, plate-based chemiluminescent method for measuring global A-to-I editing signatures in cellular RNA. We first optimize and validate our assay with chemically synthesized oligonucleotides. We then demonstrate rapid detection of inosine content in treated cell lines, demonstrating equivalent performance against current standard RNA-seq approaches. Lastly, we deploy our EndoVLISA for profiling differential A-to-I RNA editing signatures in normal and diseased human tissue, illustrating the utility of our platform as a diagnostic bioassay. Together, the EndoVLISA method is cost-effective, straightforward, and utilizes common laboratory equipment, offering a highly accessible new approach for studying A-to-I editing. Moreover, the multi-well plate format makes this the first assay amenable for direct high-throughput quantification of A-to-I editing for applications in disease detection and drug development.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
| | - Robert A Arthur
- Emory Integrated Computational Core, Emory University, 101 Woodruff Cir., Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, 1365 Clifton Rd, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Emory Integrated Computational Core, Emory University, 101 Woodruff Cir., Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, 1365 Clifton Rd, Atlanta, GA, 30322, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
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21
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Direct Immunodetection of Global A‐to‐I RNA Editing Activity with a Chemiluminescent Bioassay. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Bartee D, Thalalla Gamage S, Link CN, Meier JL. Arrow pushing in RNA modification sequencing. Chem Soc Rev 2021; 50:9482-9502. [PMID: 34259263 DOI: 10.1039/d1cs00214g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methods to accurately determine the location and abundance of RNA modifications are critical to understanding their functional role. In this review, we describe recent efforts in which chemical reactivity and next-generation sequencing have been integrated to detect modified nucleotides in RNA. For eleven exemplary modifications, we detail chemical, enzymatic, and metabolic labeling protocols that can be used to differentiate them from canonical nucleobases. By emphasizing the molecular rationale underlying these detection methods, our survey highlights new opportunities for chemistry to define the role of RNA modifications in disease.
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Affiliation(s)
- David Bartee
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Courtney N Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
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23
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Knutson SD, Heemstra JM. EndoVIPER-seq for Improved Detection of A-to-I Editing Sites in Cellular RNA. ACTA ACUST UNITED AC 2021; 12:e82. [PMID: 32469473 DOI: 10.1002/cpch.82] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Adenosine to-inosine (A-to-I) RNA editing is a conserved post-transcriptional modification that is critical for a variety of cellular processes. A-to-I editing is widespread in nearly all types of RNA, directly imparting significant global changes in cellular function and behavior. Dysfunctional RNA editing is also implicated in a number of diseases, and A-to-I editing activity is rapidly becoming an important biomarker for early detection of cancer, immune disorders, and neurodegeneration. While millions of sites have been identified, the biological function of the majority of these sites is unknown, and the regulatory mechanisms for controlling editing activity at individual sites is not well understood. Robust detection and mapping of A-to-I editing activity throughout the transcriptome is vital for understanding these properties and how editing affects cellular behavior. However, accurately identifying A-to-I editing sites is challenging because of inherent sampling errors present in RNA-seq. We recently developed Endonuclease V immunoprecipitation enrichment sequencing (EndoVIPER-seq) to directly address this challenge by enrichment of A-to-I edited RNAs prior to sequencing. This protocol outlines how to process cellular RNA, enrich for A-to-I edited transcripts with EndoVIPER pulldown, and prepare libraries suitable for generating RNA-seq data. © 2020 Wiley Periodicals LLC. Basic Protocol 1: mRNA fragmentation and glyoxalation Basic Protocol 2: EndoVIPER pulldown Basic Protocol 3: RNA-seq library preparation and data analysis.
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24
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Marceca GP, Tomasello L, Distefano R, Acunzo M, Croce CM, Nigita G. Detecting and Characterizing A-To-I microRNA Editing in Cancer. Cancers (Basel) 2021; 13:1699. [PMID: 33916692 PMCID: PMC8038323 DOI: 10.3390/cancers13071699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.
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Affiliation(s)
- Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, 95125 Catania, Italy
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
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25
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Wang H, Chen S, Wei J, Song G, Zhao Y. A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects. Front Oncol 2021; 10:632187. [PMID: 33643923 PMCID: PMC7905090 DOI: 10.3389/fonc.2020.632187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
As an important regulatory mechanism at the posttranscriptional level in metazoans, adenosine deaminase acting on RNA (ADAR)-induced A-to-I RNA editing modification of double-stranded RNA has been widely detected and reported. Editing may lead to non-synonymous amino acid mutations, RNA secondary structure alterations, pre-mRNA processing changes, and microRNA-mRNA redirection, thereby affecting multiple cellular processes and functions. In recent years, researchers have successfully developed several bioinformatics software tools and pipelines to identify RNA editing sites. However, there are still no widely accepted editing site standards due to the variety of parallel optimization and RNA high-seq protocols and programs. It is also challenging to identify RNA editing by normal protocols in tumor samples due to the high DNA mutation rate. Numerous RNA editing sites have been reported to be located in non-coding regions and can affect the biosynthesis of ncRNAs, including miRNAs and circular RNAs. Predicting the function of RNA editing sites located in non-coding regions and ncRNAs is significantly difficult. In this review, we aim to provide a better understanding of bioinformatics strategies for human cancer A-to-I RNA editing identification and briefly discuss recent advances in related areas, such as the oncogenic and tumor suppressive effects of RNA editing.
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Affiliation(s)
- Heming Wang
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, China
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Sinuo Chen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Jiayi Wei
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Guangqi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Liver Diseases, Shanghai, China
| | - Yicheng Zhao
- Clinical Medical College, Changchun University of Chinese Medicine, Changchun, China
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26
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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