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Ding JH, Li G, Xiong J, Liu FL, Xie NB, Ji TT, Wang M, Guo X, Feng YQ, Ci W, Yuan BF. Whole-Genome Mapping of Epigenetic Modification of 5-Formylcytosine at Single-Base Resolution by Chemical Labeling Enrichment and Deamination Sequencing. Anal Chem 2024; 96:4726-4735. [PMID: 38450632 DOI: 10.1021/acs.analchem.4c00425] [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: 03/08/2024]
Abstract
DNA cytosine methylation (5-methylcytosine, 5mC) is a predominant epigenetic modification that plays a critical role in a variety of biological and pathological processes in mammals. In active DNA demethylation, the 10-11 translocation (TET) dioxygenases can sequentially oxidize 5mC to generate three modified forms of cytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Beyond being a demethylation intermediate, recent studies have shown that 5fC has regulatory functions in gene expression and chromatin organization. While some methods have been developed to detect 5fC, genome-wide mapping of 5fC at base resolution is still highly desirable. Herein, we propose a chemical labeling enrichment and deamination sequencing (CLED-seq) method for detecting 5fC in genomic DNA at single-base resolution. The CLED-seq method utilizes selective labeling and enrichment of 5fC-containing DNA fragments, followed by deamination mediated by apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (APOBEC3A or A3A) and sequencing. In the CLED-seq process, while all C, 5mC, and 5hmC are interpreted as T during sequencing, 5fC is still read as C, enabling the precise detection of 5fC in DNA. Using the proposed CLED-seq method, we accomplished genome-wide mapping of 5fC in mouse embryonic stem cells. The mapping study revealed that promoter regions enriched with 5fC overlapped with H3K4me1, H3K4me3, and H3K27ac marks. These findings suggest a correlation between 5fC marks and active gene expression in mESCs. In conclusion, CLED-seq is a straightforward, bisulfite-free method that offers a valuable tool for detecting 5fC in genomes at a single-base resolution.
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Affiliation(s)
- Jiang-Hui Ding
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Gaojie Li
- Key Laboratory of Genomics and Precision Medicine, and China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiong
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Fei-Long Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Neng-Bin Xie
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Qi Feng
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, and China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bi-Feng Yuan
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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Guo X, Xie NB, Chen W, Ji TT, Xiong J, Feng T, Wang M, Zhang S, Gu SY, Feng YQ, Yuan BF. AlkB-Facilitated Demethylation Enables Quantitative and Site-Specific Detection of Dual Methylation of Adenosine in RNA. Anal Chem 2024; 96:847-855. [PMID: 38159051 DOI: 10.1021/acs.analchem.3c04457] [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: 01/03/2024]
Abstract
RNA molecules undergo various chemical modifications that play critical roles in a wide range of biological processes. N6,N6-Dimethyladenosine (m6,6A) is a conserved RNA modification and is essential for the processing of rRNA. To gain a deeper understanding of the functions of m6,6A, site-specific and accurate quantification of this modification in RNA is indispensable. In this study, we developed an AlkB-facilitated demethylation (AD-m6,6A) method for the site-specific detection and quantification of m6,6A in RNA. The N6,N6-dimethyl groups in m6,6A can cause reverse transcription to stall at the m6,6A site, resulting in truncated cDNA. However, we found that Escherichia coli AlkB demethylase can effectively demethylate m6,6A in RNA, generating full-length cDNA from AlkB-treated RNA. By quantifying the amount of full-length cDNA produced using quantitative real-time PCR, we were able to achieve site-specific detection and quantification of m6,6A in RNA. Using the AD-m6,6A method, we successfully detected and quantified m6,6A at position 1851 of 18S rRNA and position 937 of mitochondrial 12S rRNA in human cells. Additionally, we found that the level of m6,6A at position 1007 of mitochondrial 12S rRNA was significantly reduced in lung tissues from sleep-deprived mice compared with control mice. Overall, the AD-m6,6A method provides a valuable tool for easy, accurate, quantitative, and site-specific detection of m6,6A in RNA, which can aid in uncovering the functions of m6,6A in human diseases.
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Affiliation(s)
- Xia Guo
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Neng-Bin Xie
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wei Chen
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Jun Xiong
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tian Feng
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Shan Zhang
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Shu-Yi Gu
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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