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—m(7)GpppN, m(7)GpppNm, GpppN, GpppNm, and m(2,2,7)GpppG—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 m(7)Gpppm(6)A), cell- and tissue-specific variations in cap methylation, and high proportions of caps lacking 2′-O-methylation (m(7)Gpppm(6)A in mammals, m(7)GpppA in dengue virus). While substantial Dimroth-induced loss of m(1)A and m(1)Am arose with specific RNA processing conditions, human lymphoblast cells showed no detectable m(1)A or m(1)Am in caps. CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps.