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Title: Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA
Authors: Wang, Jin
Chew, Alvin Bing Liang
Lai, Yong
Dong, Hongping
Xu, Luang
Balamkundu, Seetharamsingh
Cai, Maggie Weiling
Cui, Liang
Liu, Chuan Fa
Fu, Xin-Yuan
Lin, Zhenguo
Shi, Pei-Yong
Lu, Timothy K.
Luo, Dahai
Jaffrey, Samie R.
Dedon, Peter C.
Keywords: Science::Medicine
Issue Date: 2019
Source: Wang, J., Chew, A. B. L., Lai, Y., Dong, H., Xu, L., Balamkundu, S., . . . Dedon, P. C. (2019). Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids Research, 47(20), e130-. doi:10.1093/nar/gkz751
Journal: Nucleic Acids Research
Abstract: 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.
ISSN: 0305-1048
DOI: 10.1093/nar/gkz751
Rights: © 2019 The Author(s) (Published by Oxford University Press on behalf of Nucleic Acids Research). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:LKCMedicine Journal Articles

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