A mass spectrometry-based method for direct determination of pseudouridine in RNA.

Abstract

Pseudouridine (5-ribosyluracil, Ψ) is the only 'mass-silent' nucleoside produced by post-transcriptional RNA modification. We describe here a novel mass spectrometry (MS)-based method for direct determination of Ψ in RNA. The method assigns a Ψ-containing nucleolytic RNA fragment by an accurate measurement of a signature doubly dehydrated nucleoside anion ([C9H7N2O4](1-),m/z207.04) produced by collision-induced dissociation MS, and it determines the Ψ-containing nucleotide sequence by pseudo-MS(3), i.e. in-source fragmentation followed by MS(2) By applying this method, we identified all of the known Ψs in the canonical human spliceosomal snRNAs and, unexpectedly, found two previously unknown Ψs in the U5 and U6 snRNAs. Because the method allows direct determination of Ψ in a subpicomole quantity of RNA, it will serve as a useful tool for the structure/function studies of a wide variety of non-coding RNAs.

DOI: 10.1093/nar/gkv1462

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Cite this paper

@article{Yamauchi2016AMS, title={A mass spectrometry-based method for direct determination of pseudouridine in RNA.}, author={Yoshio Yamauchi and Yuko Nobe and Keiichi Izumikawa and Daisuke Higo and Yoko Yamagishi and Nobuhiro Takahashi and Hiroshi Nakayama and Toshiaki Isobe and Masato Taoka}, journal={Nucleic acids research}, year={2016}, volume={44 6}, pages={e59} }