Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA
Chemical modification of transcripts with 5' caps occurs in all organisms. Here, we report a systems-level mass spectrometry-based technique, CapQuant, for quantitative analysis of an organism's cap epitranscriptome. The method was piloted with 21 canonical caps-m7GpppN, m7GpppNm, GpppN, G...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press (OUP)
2020
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| Online Access: | https://hdl.handle.net/1721.1/126288 |
| _version_ | 1811093364632715264 |
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| author | Wang, Jin Alvin Chew, Bing Liang Lai, Yong Dong, Hongping Xu, Luang Balamkundu, Seetharamsingh Cai, Weiling Maggie Cui, Liang Liu, Chuan Fa Fu, Xin-Yuan Lin, Zhenguo Shi, Pei-Yong Lu, Timothy K Luo, Dahai Jaffrey, Samie R Dedon, Peter C |
| author2 | Massachusetts Institute of Technology. Synthetic Biology Center |
| author_facet | Massachusetts Institute of Technology. Synthetic Biology Center Wang, Jin Alvin Chew, Bing Liang Lai, Yong Dong, Hongping Xu, Luang Balamkundu, Seetharamsingh Cai, Weiling Maggie Cui, Liang Liu, Chuan Fa Fu, Xin-Yuan Lin, Zhenguo Shi, Pei-Yong Lu, Timothy K Luo, Dahai Jaffrey, Samie R Dedon, Peter C |
| author_sort | Wang, Jin |
| collection | MIT |
| description | Chemical modification of transcripts with 5' caps occurs in all organisms. Here, we report a systems-level mass spectrometry-based technique, CapQuant, for quantitative analysis of an organism's cap epitranscriptome. The method was piloted with 21 canonical caps-m7GpppN, m7GpppNm, GpppN, GpppNm, and m2,2,7GpppG-and 5 'metabolite' caps-NAD, FAD, UDP-Glc, UDP-GlcNAc, and dpCoA. Applying CapQuant to RNA from purified dengue virus, Escherichia coli, yeast, mouse tissues, and human cells, we discovered new cap structures in humans and mice (FAD, UDP-Glc, UDP-GlcNAc, and m7Gpppm6A), cell- and tissue-specific variations in cap methylation, and high proportions of caps lacking 2'-O-methylation (m7Gpppm6A in mammals, m7GpppA in dengue virus). While substantial Dimroth-induced loss of m1A and m1Am arose with specific RNA processing conditions, human lymphoblast cells showed no detectable m1A or m1Am in caps. CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps. |
| first_indexed | 2024-09-23T15:44:05Z |
| format | Article |
| id | mit-1721.1/126288 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T15:44:05Z |
| publishDate | 2020 |
| publisher | Oxford University Press (OUP) |
| record_format | dspace |
| spelling | mit-1721.1/1262882022-09-29T15:49:16Z Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA Wang, Jin Alvin Chew, Bing Liang Lai, Yong Dong, Hongping Xu, Luang Balamkundu, Seetharamsingh Cai, Weiling Maggie Cui, Liang Liu, Chuan Fa Fu, Xin-Yuan Lin, Zhenguo Shi, Pei-Yong Lu, Timothy K Luo, Dahai Jaffrey, Samie R Dedon, Peter C Massachusetts Institute of Technology. Synthetic Biology Center Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Chemical modification of transcripts with 5' caps occurs in all organisms. Here, we report a systems-level mass spectrometry-based technique, CapQuant, for quantitative analysis of an organism's cap epitranscriptome. The method was piloted with 21 canonical caps-m7GpppN, m7GpppNm, GpppN, GpppNm, and m2,2,7GpppG-and 5 'metabolite' caps-NAD, FAD, UDP-Glc, UDP-GlcNAc, and dpCoA. Applying CapQuant to RNA from purified dengue virus, Escherichia coli, yeast, mouse tissues, and human cells, we discovered new cap structures in humans and mice (FAD, UDP-Glc, UDP-GlcNAc, and m7Gpppm6A), cell- and tissue-specific variations in cap methylation, and high proportions of caps lacking 2'-O-methylation (m7Gpppm6A in mammals, m7GpppA in dengue virus). While substantial Dimroth-induced loss of m1A and m1Am arose with specific RNA processing conditions, human lymphoblast cells showed no detectable m1A or m1Am in caps. CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps. 2020-07-21T18:51:32Z 2020-07-21T18:51:32Z 2019-09 2019-07 2020-03-05T17:32:34Z Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 https://hdl.handle.net/1721.1/126288 Wang, Jin et al. "Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA." Nucleic Acids Research 47, 20 (September 2020): e130 © 2019 The Author(s) en http://dx.doi.org/10.1093/nar/gkz751 Nucleic Acids Research Creative Commons Attribution NonCommercial License 4.0 https://creativecommons.org/licenses/by-nc/4.0/ application/pdf Oxford University Press (OUP) Nucleic Acids Research |
| spellingShingle | Wang, Jin Alvin Chew, Bing Liang Lai, Yong Dong, Hongping Xu, Luang Balamkundu, Seetharamsingh Cai, Weiling Maggie Cui, Liang Liu, Chuan Fa Fu, Xin-Yuan Lin, Zhenguo Shi, Pei-Yong Lu, Timothy K Luo, Dahai Jaffrey, Samie R Dedon, Peter C Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA |
| title | Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA |
| title_full | Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA |
| title_fullStr | Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA |
| title_full_unstemmed | Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA |
| title_short | Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA |
| title_sort | quantifying the rna cap epitranscriptome reveals novel caps in cellular and viral rna |
| url | https://hdl.handle.net/1721.1/126288 |
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