High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome
Abstract N 6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Publishing Group
2022-12-01
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| Series: | Cell Discovery |
| Online Access: | https://doi.org/10.1038/s41421-022-00484-1 |
| _version_ | 1828083507601080320 |
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| author | Li-Qian Chen Zhang Zhang Hong-Xuan Chen Jian-Fei Xi Xue-Hong Liu Dong-Zhao Ma Yu-Hao Zhong Wen Hui Ng Tao Chen Daniel W. Mak Qi Chen Yao-Qing Chen Guan-Zheng Luo |
| author_facet | Li-Qian Chen Zhang Zhang Hong-Xuan Chen Jian-Fei Xi Xue-Hong Liu Dong-Zhao Ma Yu-Hao Zhong Wen Hui Ng Tao Chen Daniel W. Mak Qi Chen Yao-Qing Chen Guan-Zheng Luo |
| author_sort | Li-Qian Chen |
| collection | DOAJ |
| description | Abstract N 6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism. |
| first_indexed | 2024-04-11T04:08:44Z |
| format | Article |
| id | doaj.art-94b9f4cbfe6a4d60a2937f9d1128ae21 |
| institution | Directory Open Access Journal |
| issn | 2056-5968 |
| language | English |
| last_indexed | 2024-04-11T04:08:44Z |
| publishDate | 2022-12-01 |
| publisher | Nature Publishing Group |
| record_format | Article |
| series | Cell Discovery |
| spelling | doaj.art-94b9f4cbfe6a4d60a2937f9d1128ae212023-01-01T12:12:52ZengNature Publishing GroupCell Discovery2056-59682022-12-018111110.1038/s41421-022-00484-1High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genomeLi-Qian Chen0Zhang Zhang1Hong-Xuan Chen2Jian-Fei Xi3Xue-Hong Liu4Dong-Zhao Ma5Yu-Hao Zhong6Wen Hui Ng7Tao Chen8Daniel W. Mak9Qi Chen10Yao-Qing Chen11Guan-Zheng Luo12MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversitySchool of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong KongSchool of Public Health (Shenzhen), Sun Yat-sen UniversitySchool of Public Health (Shenzhen), Sun Yat-sen UniversityMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen UniversityAbstract N 6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.https://doi.org/10.1038/s41421-022-00484-1 |
| spellingShingle | Li-Qian Chen Zhang Zhang Hong-Xuan Chen Jian-Fei Xi Xue-Hong Liu Dong-Zhao Ma Yu-Hao Zhong Wen Hui Ng Tao Chen Daniel W. Mak Qi Chen Yao-Qing Chen Guan-Zheng Luo High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome Cell Discovery |
| title | High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome |
| title_full | High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome |
| title_fullStr | High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome |
| title_full_unstemmed | High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome |
| title_short | High-precision mapping reveals rare N 6 -deoxyadenosine methylation in the mammalian genome |
| title_sort | high precision mapping reveals rare n 6 deoxyadenosine methylation in the mammalian genome |
| url | https://doi.org/10.1038/s41421-022-00484-1 |
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