1. Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA
- Author
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Weiling Maggie Cai, Jin Wang, Zhenguo Lin, Liang Cui, Hongping Dong, Luang Xu, Samie R. Jaffrey, Timothy K. Lu, Seetharamsingh Balamkundu, Dahai Luo, Peter C. Dedon, Chuan-Fa Liu, Bing Liang Alvin Chew, Yong Lai, Pei Yong Shi, Xin-Yuan Fu, School of Biological Sciences, Interdisciplinary Graduate School (IGS), Lee Kong Chian School of Medicine (LKCMedicine), and NTU Institute of Health Technologies
- Subjects
RNA Caps ,Sequence analysis ,Mass Spectrometry-based Technique ,Metabolite ,Saccharomyces cerevisiae ,Biology ,Dengue virus ,medicine.disease_cause ,RNA Characterisation and Manipulation ,Epigenesis, Genetic ,Transcriptome ,03 medical and health sciences ,Mice ,chemistry.chemical_compound ,Genetics ,medicine ,Animals ,Humans ,Medicine [Science] ,Nucleotide ,RNA Processing, Post-Transcriptional ,Escherichia coli ,Cells, Cultured ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Sequence Analysis, RNA ,030302 biochemistry & molecular biology ,Eukaryotic transcription ,RNA ,Methylation ,Dengue Virus ,Yeast ,Mice, Inbred C57BL ,carbohydrates (lipids) ,chemistry ,Biochemistry ,Methods Online ,RNA, Viral ,Female - 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 the cap epitranscriptome in any organism. 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, mice, and humans, we discovered four new cap structures in humans and mice (FAD, UDP-Glc, UDP-GlcNAc, and m7Gpppm6A), cell- and tissue-specific variations in cap methylation, and surprisingly high proportions of caps lacking 2’-O-methylation, such as m7Gpppm6A in mammals and m7GpppA in dengue virus, and we did not detect cap m1A/m1Am in humans. CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps. The mystery around cap m1A/m1Am analysis remains unresolved.
- Published
- 2019
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