Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution
- Resource Type
- Article
- Authors
- Dai, Qing; Zhang, Li-Sheng; Sun, Hui-Lung; Pajdzik, Kinga; Yang, Lei; Ye, Chang; Ju, Cheng-Wei; Liu, Shun; Wang, Yuru; Zheng, Zhong; Zhang, Linda; Harada, Bryan T.; Dou, Xiaoyang; Irkliyenko, Iryna; Feng, Xinran; Zhang, Wen; Pan, Tao; He, Chuan
- Source
- Nature Biotechnology; March 2023, Vol. 41 Issue: 3 p344-354, 11p
- Subject
- Language
- ISSN
- 10870156; 15461696
Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10–20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different ‘writer’ proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.