Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA-Reference-Cited by-同舟云学术

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA

Published:2019-09-02 Issue:20 Volume:47 Page:e130-e130
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Wang Jin¹²³,Alvin Chew Bing Liang³⁴⁵,Lai Yong³,Dong Hongping⁶,Xu Luang⁷,Balamkundu Seetharamsingh³⁸,Cai Weiling Maggie³⁹,Cui Liang³,Liu Chuan Fa⁸,Fu Xin-Yuan⁷,Lin Zhenguo¹⁰,Shi Pei-Yong¹¹,Lu Timothy K³¹²^ORCID,Luo Dahai⁴^ORCID,Jaffrey Samie R¹³,Dedon Peter C³¹⁴

Affiliation:

1. State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, People's Republic of China

2. School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China

3. Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore

4. Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore

5. NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore

6. Shanghai Blueray Biopharma, Shanghai, People's Republic of China

7. Cancer Science Institute of Singapore, Singapore

8. School of Biological Sciences, Nanyang Technological University, Singapore

9. Department of Microbiology, National University of Singapore, Singapore

10. Department of Biology, Saint Louis University, St. Louis, MO, USA

11. Departments of Biochemistry & Molecular Biology and Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA

12. Synthetic Biology Center, Departments of Biological Engineering and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA

13. Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA

14. Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

Abstract

AbstractChemical 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.

Funder

National Institutes of Health

National Research Foundation of Singapore

Inner Mongolia University

Nanyang Presidential Graduate Scholarship

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/article-pdf/47/20/e130/30623663/gkz751.pdf

Reference77 articles.