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.
- Downloaded 730 times
- Download rankings, all-time:
- Site-wide: 37,048
- In systems biology: 808
- Year to date:
- Site-wide: 111,819
- Since beginning of last month:
- Site-wide: 87,616
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!