假尿苷
转录组
生物
核糖核酸
计算生物学
小核仁RNA
N6-甲基腺苷
基因
基因表达
遗传学
长非编码RNA
甲基化
转移RNA
甲基转移酶
作者
Meiling Zhang,Zhe Jiang,Yichen Ma,Wenqing Liu,Yuan Zhuang,Bo Lu,Kai Li,Peng Ji,Chengqi Yi
标识
DOI:10.1038/s41589-023-01304-7
摘要
Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, stoichiometric measurement of individual Ψ sites in human transcriptome remains unaddressed. Here we develop 'PRAISE', via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional bisulfite treatment, our approach is based on quaternary base mapping and revealed an ~10% median modification level for 2,209 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7, TRUB1 and DKC1, with TRUB1 targets showing the highest modification stoichiometry. In addition, we quantified known and new Ψ sites in mitochondrial mRNA catalyzed by PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide Ψ; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.
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