Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA
Bing Liang Alvin Chew,
Weiling Maggie Cai,
Chuan Fa Liu,
Timothy K Lu,
Samie R. Jaffrey,
Peter C. Dedon
Posted 03 Jul 2019
bioRxiv DOI: 10.1101/683045 (published DOI: 10.1093/nar/gkz751)
Posted 03 Jul 2019
Chemical modification of transcripts with 5 prime 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.
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