A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome

Pei-Yong Shi, Luang Xu, Jin Wang, Bing Liang Alvin Chew, Yong Lai, Hongping Dong, Yu Liu, Xin-Yuan Fu, Zhenguo Lin, Timothy K. Lu, Dahai Luo, Samie R. Jaffrey, Peter C. Dedon

Published: 2023-08-10 DOI: 10.1038/s41596-023-00857-0

RNA cap epitranscriptome

Mass spectrometry

CapQuant

Stable isotope-labeled cap nucleotides

Quantification

AI 解读

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Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- Reporting summary
Acknowledgements

Villalta, P. W. & Balbo, S. The future of DNA adductomic analysis. Int. J. Mol. Sci. 18, 1870 (2017).
Dominissini, D. et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441–446 (2016).
Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol. 12, 311–316 (2016).
Safra, M. et al. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature 551, 251–255 (2017).
Dong, H. et al. 2′-O methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS Pathog. 8, e1002642 (2012).
Murata, M. et al. in Transcription Factor Regulatory Networks: Methods and Protocols. (eds E. Miyamoto-Sato et al.) 67–85 (Springer, 2014).
Kanamori-Katayama, M. et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 21, 1150–1159 (2011).
Lu, Z. & Lin, Z. Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. Genome Res. 29, 1198–1210 (2019).
Lizio, M. et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 16, 22 (2015).
Lizio, M. et al. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 45, D737–D743 (2017).
Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46, W537–W544 (2018).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Mauer, J. et al. Reversible methylation of m6Am in the 5′ cap controls mRNA stability. Nature 541, 371–375 (2017).
Helm, M. & Alfonzo, J. D. Posttranscriptional RNA modifications: playing metabolic games in a cell’s chemical Legoland. Chem. Biol. 21, 174–185 (2014).
Ramanathan, A., Robb, G. B. & Chan, S. H. mRNA capping: biological functions and applications. Nucleic Acids Res. 44, 7511–7526 (2016).
Hyde, J. L. & Diamond, M. S. Innate immune restriction and antagonism of viral RNA lacking 2-O methylation. Virology 479–480, 66–74 (2015).
Kastern, W. H. & Berry, S. J. Non-methylated guanosine as 5′ terminus of capped messenger-rna from insect oocytes. Biochem. Biophys. Res. Commun. 71, 37–44 (1976).
Wei, C., Gershowitz, A. & Moss, B. N6, O2′-dimethyladenosine a novel methylated ribonucleoside next to the 5′ terminal of animal cell and virus mRNAs. Nature 257, 251–253 (1975).
HsuChen, C. C. & Dubin, D. T. Di-and trimethylated congeners of 7-methylguanine in Sindbis virus mRNA. Nature 264, 190–191 (1976).
Byszewska, M., Smietanski, M., Purta, E. & Bujnicki, J. M. RNA methyltransferases involved in 5′ cap biosynthesis. RNA Biol. 11, 1597–1607 (2014).
Bird, J. G. et al. The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature 535, 444–447 (2016).
Julius, C. & Yuzenkova, Y. Bacterial RNA polymerase caps RNA with various cofactors and cell wall precursors. Nucleic Acids Res. 45, 8282–8290 (2017).
Jaschke, A., Hofer, K., Nubel, G. & Frindert, J. Cap-like structures in bacterial RNA and epitranscriptomic modification. Curr. Opin. Microbiol. 30, 44–49 (2016).
Kiledjian, M. Eukaryotic RNA 5′-end NAD+ capping and DeNADding. Trends Cell Biol. 28, 454–464 (2018).
Yu, X. et al. Messenger RNA 5′ NAD+ capping is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in arabidopsis. Dev. Cell 56, 125–140 e126 (2021).
Wang, J. et al. Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids Res. 47, e130 (2019).
Abraham, G., Rhodes, D. P. & Banerjee, A. K. The 5′ terminal structure of the methylated mRNA synthesized in vitro by vesicular stomatitis virus. Cell 5, 51–58 (1975).
Mauer, J. et al. Reversible methylation of m(6)Am in the 5′ cap controls mRNA stability. Nature 541, 371–375 (2017).
Topisirovic, I., Svitkin, Y. V., Sonenberg, N. & Shatkin, A. J. Cap and cap-binding proteins in the control of gene expression. Wiley Interdiscip. Rev. RNA 2, 277–298 (2011).
Adams, N. M. et al. Comparison of three magnetic bead surface functionalities for RNA extraction and detection. ACS Appl. Mater. Interfaces 7, 6062–6069 (2015).
Furuichi, Y. Discovery of m7G-cap in eukaryotic mRNAs. Proc. Jpn Acad. Ser. B 91, 394–409 (2015).
Shatkin, A. J. Capping of eucaryotic mRNAs. Cell 9, 645–653 (1976).
Wei, C. M., Gershowitz, A. & Moss, B. 5′-Terminal and internal methylated nucleotide sequences in HeLa cell mRNA. Biochemistry 15, 397–401 (1976).
Cleaver, J. E. & Burki, H. J. Letter: biological damage from intranuclear carbon-14 decays: DNA single-strand breaks and repair in mammalian cells. Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 26, 399–403 (1974).
Minor, R. R. Cytotoxic effects of low levels of 3H-, 14C-, and 35S-labeled amino acids. J. Biol. Chem. 257, 10400–10413 (1982).
Abdelhamid, R. F. et al. Multiplicity of 5′ cap structures present on short RNAs. PLoS ONE 9, e102895 (2014).
Akichika, S. et al. Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science 363, eaav0080 (2019).
Beverly, M., Dell, A., Parmar, P. & Houghton, L. Label-free analysis of mRNA capping efficiency using RNase H probes and LC–MS. Anal. Bioanal. Chem. 408, 5021–5030 (2016).
Chen, Y. G., Kowtoniuk, W. E., Agarwal, I., Shen, Y. & Liu, D. R. LC/MS analysis of cellular RNA reveals NAD-linked RNA. Nat. Chem. Biol. 5, 879–881 (2009).
Ohira, T. & Suzuki, T. Precursors of tRNAs are stabilized by methylguanosine cap structures. Nat. Chem. Biol. 12, 648–655 (2016).
Peyrane, F. et al. High-yield production of short GpppA- and (7Me)GpppA-capped RNAs and HPLC-monitoring of methyltransfer reactions at the guanine-N7 and adenosine-2′O positions. Nucleic Acids Res. 35, e26 (2007).
Cahova, H., Winz, M.-L., Höfer, K., Nübel, G. & Jäschke, A. NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature 519, 374–377 (2015).
Shao, X. et al. NAD tagSeq for transcriptome-wide identification and characterization of NAD+-capped RNAs. Nat. Protoc. 15, 2813–2836 (2020).
Hu, H. et al. SPAAC-NAD-seq, a sensitive and accurate method to profile NAD(+)-capped transcripts. Proc. Natl Acad. Sci. USA http://doi.org/10.1073/pnas.2025595118 (2021).
Galloway, A. et al. CAP-MAP: cap analysis protocol with minimal analyte processing, a rapid and sensitive approach to analysing mRNA cap structures. Open Biol. 10, 190306 (2020).
Gao, Y., Bu, J., Peng, Z. & Yang, B. Radical reactions in the gas phase: recent development and application in biomolecules. J. Spectrosc. http://doi.org/10.1155/2014/570863 (2014).
Hu, J., Lei, W., Wang, J., Chen, H. Y. & Xu, J. J. Regioselective 5′-position phosphorylation of ribose and ribonucleosides: phosphate transfer in the activated pyrophosphate complex in the gas phase. Chem. Commun. 55, 310–313 (2019).
Strzelecka, D., Chmielinski, S., Bednarek, S., Jemielity, J. & Kowalska, J. Analysis of mononucleotides by tandem mass spectrometry: investigation of fragmentation pathways for phosphate- and ribose-modified nucleotide analogues. Sci. Rep. 7, 8931 (2017).
Grudzien-Nogalska, E., Bird, J. G., Nickels, B. E. & Kiledjian, M. “NAD-capQ” detection and quantitation of NAD caps. RNA 24, 1418–1425 (2018).
Moya-Ramirez, I., Bouton, C., Kontoravdi, C. & Polizzi, K. High resolution biosensor to test the capping level and integrity of mRNAs. Nucleic Acids Res. 48, e129 (2020).
Liu, S. & Wang, Y. Mass spectrometry for the assessment of the occurrence and biological consequences of DNA adducts. Chem. Soc. Rev. 44, 7829–7854 (2015).

A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome

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