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Zhang Z, He T, Qi Y, Dai Y, Lao K, Gou X. Rapid and highly specific detection of site-specific 5-hydroxymethylcytosine based on peroxotungstate oxidation and mismatch ligation-based LAMP. RSC Adv 2022; 12:19885-19889. [PMID: 35865199 PMCID: PMC9261916 DOI: 10.1039/d2ra03310k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
We have developed a rapid and specific method for site-specific 5-hydroxymethylcytosine (5hmC) quantification at single-base resolution. This bisulfite-free method integrates the peroxotungstate oxidization with the mismatched probe-assisted ligation to guarantee the specificity. Moreover, the high-efficiency LAMP also makes the proposed method suitable for the detection of low-content samples. A facile and highly specific mismatch ligation-based amplification platform for quantification of site-specific 5hmC at single base resolution in low-content samples.![]()
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Affiliation(s)
- Zhenhao Zhang
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Tong He
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Yan Qi
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Yuxuan Dai
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Kejing Lao
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
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2
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Liu H, Wang Y, Zhou X. Labeling and sequencing nucleic acid modifications using bio-orthogonal tools. RSC Chem Biol 2022; 3:994-1007. [PMID: 35975003 PMCID: PMC9347354 DOI: 10.1039/d2cb00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
The bio-orthogonal reaction is a type of reaction that can occur within a cell without interfering with the active components of the cell. Bio-orthogonal reaction techniques have been used to label and track the synthesis, metabolism, and interactions of distinct biomacromolecules in cells. Thus, it is a handy tool for analyzing biological macromolecules within cells. Nucleic acid modifications are widely distributed in DNA and RNA in cells and play a critical role in regulating physiological and pathological cellular activities. Utilizing bio-orthogonal tools to study modified bases is a critical and worthwhile research direction. The development of bio-orthogonal reactions focusing on nucleic acid modifications has enabled the mapping of nucleic acid modifications in DNA and RNA. This review discusses the recent advances in bio-orthogonal labeling and sequencing nucleic acid modifications in DNA and RNA. Labeling nucleic acid modifications using bio-orthogonal tools, then sequencing and imaging the labeled modifications in DNA and RNA.![]()
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Affiliation(s)
- Hui Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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3
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Guo G, Pan K, Fang S, Ye L, Tong X, Wang Z, Xue X, Zhang H. Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:575-593. [PMID: 34631286 PMCID: PMC8479277 DOI: 10.1016/j.omtn.2021.08.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-methylcytosine (m5C) post-transcriptional modifications affect the maturation, stability, and translation of the mRNA molecule. These modifications play an important role in many physiological and pathological processes, including stress response, tumorigenesis, tumor cell migration, embryogenesis, and viral replication. Recently, there has been a better understanding of the biological implications of m5C modification owing to the rapid development and optimization of detection technologies, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-BisSeq. Further, predictive models (such as PEA-m5C, m5C-PseDNC, and DeepMRMP) for the identification of potential m5C modification sites have also emerged. In this review, we summarize the current experimental detection methods and predictive models for mRNA m5C modifications, focusing on their advantages and limitations. We systematically surveyed the latest research on the effectors related to mRNA m5C modifications and their biological functions in multiple species. Finally, we discuss the physiological effects and pathological significance of m5C modifications in multiple diseases, as well as their therapeutic potential, thereby providing new perspectives for disease treatment and prognosis.
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Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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4
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Dai Y, Yuan BF, Feng YQ. Quantification and mapping of DNA modifications. RSC Chem Biol 2021; 2:1096-1114. [PMID: 34458826 PMCID: PMC8341653 DOI: 10.1039/d1cb00022e] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.
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Affiliation(s)
- Yi Dai
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
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5
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Koyama K, Hayashi G, Ueda H, Ota S, Nagae G, Aburatani H, Okamoto A. Base-resolution analysis of 5-hydroxymethylcytidine by selective oxidation and reverse transcription arrest. Org Biomol Chem 2021; 19:6478-6486. [PMID: 34241617 DOI: 10.1039/d1ob00995h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While 5-hydroxymethylcytidine in RNA (hm5C) is associated with cellular development and differentiation, its distribution and biological function remain largely unexplored because suitable detection methods are lacking. Here, we report a base-resolution sequencing method for hm5C in RNA by applying peroxotungstate-mediated chemical conversion of hm5C to trihydroxylated thymine (thT). Reverse transcription by SuperScript III terminated at the thT site, probably because of its unnatural nucleobase structure producing truncated cDNA. Consequently, base-resolution analysis of the hm5C sites in RNA was achieved with both Sanger sequencing and Illumina sequencing analysis by comparing sequencing data before and after peroxotungstate treatment.
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Affiliation(s)
- Kenta Koyama
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Nagoya University, Furo-cho Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiroki Ueda
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Satoshi Ota
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Genta Nagae
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. and Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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6
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Ma Y, Zhang N, Chen S, Sun J, Liu Y, Li X, Wang H. One-pot intramolecular cyclization of 5-hydroxymethylcytosine for sequencing DNA hydroxymethylation at single-base resolution. Analyst 2021; 146:820-824. [PMID: 33393539 DOI: 10.1039/d0an01981j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we establish a one-pot reaction to directly convert the DNA base 5-hydroxymethylcytosine (5hmC) to an intramolecular cyclization nucleobase, which loses both protons of the exocyclic N4-amino group and thus is recognized as thymine (T) by DNA polymerase. Based on this 5hmC-specific reaction, a prospective bisulfite-free strategy for 5hmC sequencing is proposed. This is also the first example to show modified DNA labeling in non-water solvent-dominant media for DNA sequencing.
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Affiliation(s)
- Yangde Ma
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, P.R. China.
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7
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Zhang Z, Yan J, Li Z. Peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) for bisulfite-free quantification of locus-specific 5-hydroxymethylcytosine. Chem Commun (Camb) 2020; 56:3111-3114. [PMID: 32090228 DOI: 10.1039/d0cc00167h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) is applied for the first time to the sensitive detection of locus-specific 5-hydroxymethylcytosine (5hmC) in DNA with low non-specific amplification. This strategy greatly shortens reaction time, improves sensitivity, and reduces non-specific amplification.
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Affiliation(s)
- Zhenhao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Jingli Yan
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
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8
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Kurinomaru T, Kojima N, Kurita R. Sequential Assessment of Multiple Epigenetic Modifications of Cytosine in Whole Genomic DNA by Surface Plasmon Resonance. Anal Chem 2019; 91:13933-13939. [PMID: 31525025 DOI: 10.1021/acs.analchem.9b03423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the discovery of the active DNA demethylation pathway in mammals, numerous efforts have been made to distinguish epigenetic cytosine variants, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). However, the rapid discrimination of multiple cytosine variants in DNA remains challenging because the conventional assays require time-consuming DNA pretreatments, such as enzymatical digestion and chemical conversion. Here we demonstrated the high-throughput discrimination of four cytosine variants in DNA by using a sequential surface-plasmon-resonance (SPR)-based immunochemical assay. The target DNAs were biotinylated in one step with a bifunctional linker 1 and robustly immobilized on a streptavidin-coated sensor surface to hold them in place during an alkali washing designed to remove residual antibodies. By repeating the injection of antibodies and washing, we achieved a sequential assessment of cytosine variants in identical DNA and identified the yield of in vitro 5mC oxidation in genomic DNA by the ten-eleven translocation 1 (TET1) enzyme. These results demonstrated that our sequential SPR-based immunochemical assay was effective for evaluating multiple epigenetic modifications in a whole genome with a single row operation without time-consuming DNA pretreatments.
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Affiliation(s)
- Takaaki Kurinomaru
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , 1-8-31 Midorigaoka , Ikeda , Osaka 563-8577 , Japan
| | - Naoshi Kojima
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER , Tsukuba Central 6, 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
| | - Ryoji Kurita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER , Tsukuba Central 6, 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
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9
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Qi C, Ding J, Yuan B, Feng Y. Analytical methods for locating modifications in nucleic acids. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Zeng H, He B, Yi C. Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA. Chembiochem 2019; 20:1898-1905. [PMID: 30809902 DOI: 10.1002/cbic.201900035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/19/2022]
Abstract
Over the past few decades, various DNA modification detection methods have been developed; many of the high-resolution methods are based on bisulfite treatment, which leads to DNA degradation, to a degree. Thus, novel bisulfite-free approaches have been developed in recent years and shown to be useful for epigenome analysis in otherwise difficult-to-handle, but important, DNA samples, such as hmC-seal and hmC-CATCH. Herein, an overview of advances in the development of epigenome sequencing methods for these important DNA modifications is provided.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Bo He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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11
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Yuan F, Bi Y, Siejka-Zielinska P, Zhou YL, Zhang XX, Song CX. Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. Chem Commun (Camb) 2019; 55:2328-2331. [PMID: 30723849 PMCID: PMC6984333 DOI: 10.1039/c9cc00274j] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/30/2019] [Indexed: 01/28/2023]
Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), two of the best-studied DNA modifications, play crucial roles in normal development and disease in mammals. Although 5-methylcytidine (m5C) and 5-hydroxymethylcytidine (hm5C) have also been identified in RNA, their distribution and biological function in RNA remain largely unexplored, due to the lack of suitable sequencing methods. Here, we report a base-resolution sequencing method for hm5C in RNA. We applied the selective oxidation of hm5C to trihydroxylated-thymine (thT) mediated by peroxotungstate. thT was subsequently converted to T during cDNA synthesis using a thermostable group II intron reverse transcriptase (TGIRT). Base-resolution analysis of the hm5C sites in RNA was performed using Sanger sequencing. Furthermore, in combination with the TET enzyme oxidation of m5C to hm5C in RNA, we expand the use of peroxotungstate oxidation to detect m5C in RNA at base-resolution. By using this method, we confirmed three known m5C sites in human tRNA, demonstrating the applicability of our method in analyzing real RNA samples.
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Affiliation(s)
- Fang Yuan
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK. and Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Ying Bi
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
| | - Paulina Siejka-Zielinska
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
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12
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Wang Y, Zhang X, Wu F, Chen Z, Zhou X. Bisulfite-free, single base-resolution analysis of 5-hydroxymethylcytosine in genomic DNA by chemical-mediated mismatch. Chem Sci 2019; 10:447-452. [PMID: 30746092 PMCID: PMC6335847 DOI: 10.1039/c8sc04272a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/11/2018] [Indexed: 01/11/2023] Open
Abstract
5-Hydroxymethylcytosine (5hmC) is known as one of the vital players in nuclear reprogramming and the process of active DNA demethylation. Although the development of whole-genome sequencing methods for modified cytosine bases has burgeoned, the easily operated gene-specific loci detection of 5hmC has rarely been reported. Herein, we present a single-base resolution approach, i.e., chemical-assisted mismatch sequencing (CAM-Seq), which, when combined with traditional oxidation and chemical labeling mediation, can be used for mapping 5hmC at base resolution. We employ chemical oxidation to transform 5hmC to 5-formylcytosine (5fC), followed by chemical labeling to induce C-to-T base changes owing to the fact that the loss of the exocyclic 4-amino group of labeled 5fC leads to C to T conversion and subsequent pairing with adenosine (A) in PCR. The feasibility of CAM-Seq is demonstrated in different synthetic oligonucleotide models as well as in part of the genome of 5hmC-rich mouse embryonic stem cells (mESCs). Moreover, the gene fragment containing 5hmC can be easily biotinylated after oxidation, showing high enrichment efficiency. Our method has the potential capability to map 5hmC in genomic DNA and thus will contribute to promoting the understanding of the epigenetic modification of 5hmC.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Fan Wu
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Zonggui Chen
- College of Life Science , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
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14
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Zeng H, He B, Xia B, Bai D, Lu X, Cai J, Chen L, Zhou A, Zhu C, Meng H, Gao Y, Guo H, He C, Dai Q, Yi C. Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution. J Am Chem Soc 2018; 140:13190-13194. [PMID: 30278133 DOI: 10.1021/jacs.8b08297] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, hmC-CATCH enabled us to detect genome-wide hydroxymethylome of human embryonic stem cells in a cost-effective manner. Further application of hmC-CATCH to cell-free DNA (cfDNA) of healthy donors and cancer patients revealed base-resolution hydroxymethylome in the human cfDNA for the first time. We anticipate that our chemical biology approach will find broad applications in hydroxymethylome analysis of limited biological and clinical samples.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Bo He
- Peking-Tsinghua Center for Life Sciences , Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871 , China
| | - Bo Xia
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Dongsheng Bai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Xingyu Lu
- Shanghai Epican Genetech, Co. Ltd., Zhangjiang Hi-Tech Park , Shanghai 201203 , China
| | - Jiabin Cai
- Department of Liver Surgery , Liver Cancer Institute, Zhongshan Hospital, Fudan University , Shanghai 200032 , China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction , Eastern Hepatobiliary Surgery Institute, Second Military Medical University , Shanghai 200438 , China
| | - Ankun Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Yun Gao
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics , School of Life Sciences, Peking University , Beijing 100871 , China
| | - Hongshan Guo
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics , School of Life Sciences, Peking University , Beijing 100871 , China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology , Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago , Chicago , Illinois 60637 , United States.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center , College of Chemistry and Molecular Engineering, Peking University , Beijing 100871 , China
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology , Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago , Chicago , Illinois 60637 , United States
| | - 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 , Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871 , 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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15
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Sueoka T, Koyama K, Hayashi G, Okamoto A. Chemistry-Driven Epigenetic Investigation of Histone and DNA Modifications. CHEM REC 2018; 18:1727-1744. [PMID: 30070422 DOI: 10.1002/tcr.201800040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022]
Abstract
In the regulation processes of gene expression, genomic DNA and nuclear proteins, including histone proteins, cooperate with each other, leading to the distinctive functions of eukaryotic cells such as pluripotency and differentiation. Chemical modification of histone proteins and DNA has been revealed as one of the major driving forces in the complicated epigenetic regulation system. However, understanding of the precise molecular mechanisms is still limited. To address this issue, researchers have proposed both biological and chemical strategies for the preparation and detection of modified proteins and nucleic acids. In this review, we focus on chemical methods around the field of epigenetics. Chemical protein synthesis has enabled the preparation of site-specifically modified histones and their successful application to various in vitro assays, which have emphasized the significance of posttranslational modifications of interest. We also review the modification-specific chemical reactions against synthetic and genomic DNA, which enabled discrimination of several modified bases at single-base resolution.
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Affiliation(s)
- Takuma Sueoka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenta Koyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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16
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Li R, Gurav DD, Wan J, Qian K. A coming era of precision diagnostics based on nano-assisted mass spectrometry. PRECISION NANOMEDICINE 2018. [DOI: 10.33218/prnano1(2).180724.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Precision diagnostics relies on omic analysis by mass spectrometry to overcome the limitation in accuracy by an individual biomarker, due to the complex nature of diseases. Recent development in nanotechnology markedly enhanced sample treatment and detection efficiency of this method. Herein, we foresee a coming era of precision diagnostics based on nano-assisted mass spectrometry. Some important progress in the field includes detection of (1) nucleic acids for genetic analysis; (2) proteins/peptides for proteomic analysis; and (3) small molecules for metabolic analysis. We anticipate that this review will be a reminder for both young and experienced researchers about the future of diagnostics and call for attention worldwide.
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Affiliation(s)
- Rongxin Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai
| | | | - JingJing Wan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai
| | - Kun Qian
- School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University
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17
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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18
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Liu C, Wang Y, Yang W, Wu F, Zeng W, Chen Z, Huang J, Zou G, Zhang X, Wang S, Weng X, Wu Z, Zhou Y, Zhou X. Fluorogenic labeling and single-base resolution analysis of 5-formylcytosine in DNA. Chem Sci 2017; 8:7443-7447. [PMID: 29163896 PMCID: PMC5674178 DOI: 10.1039/c7sc03685j] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/04/2017] [Indexed: 12/13/2022] Open
Abstract
5-Formylcytosine (5fC), which plays an important role in epigenetic functions, has received widespread attention in many related fields. Here, we demonstrate a new design for both the fluorogenic switch-on detection and single-base resolution analysis of 5fC through selectively reacting a reagent with 5fC to yield an intramolecular cyclization nucleobase. The generated product, bearing a similar benzothiazole-iminocoumarin scaffold, is highly fluorescent and enables us to qualitatively and quantitatively detect 5fC moieties in γ-irradiated calf thymus DNA. Additionally, losing the exocyclic 4-amino group in 5fC causes the incorporation of dATP through base pairing with the generated nucleobase during polymerase extension, which helped us to analyze the 5fC sites in both single- and double-stranded oligonucleotides. Our Sanger and Illumina sequencing results show great potential in single-base resolution analysis of 5fC. It is hopeful that a similar design may be used for more detection targets.
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Affiliation(s)
- Chaoxing Liu
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Yafen Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Wei Yang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Fan Wu
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Weiwu Zeng
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Zonggui Chen
- College of Life Science , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Jinguo Huang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Zhiguo Wu
- College of Life Science , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Yu Zhou
- College of Life Science , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
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19
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Raiber EA, Hardisty R, van Delft P, Balasubramanian S. Mapping and elucidating the function of modified bases in DNA. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0069] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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20
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Abstract
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation. Additionally, many regulatory mechanisms of this process have been identified. Technological advances in mapping and tracing the oxidized forms of 5mC allow further dissection of their functions. Furthermore, the biological functions of active DNA demethylation in various biological contexts have also been revealed. In this Review, we summarize the recent advances and highlight key unanswered questions.
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