Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Issue 20 (2nd September 2019)

• Record Type: Journal Article
• Authors: 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
• Is Part Of: Nucleic acids research. Volume 47:Issue 20(2019)
• Page Start: e130
• Page End: e130
• Publication Date: 2019-09-02
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkz751
• Languages: English
• ISSNs: 0305-1048

Abstract

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—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.