Quantitative profiling of pseudouridylation landscape in the human transcriptome

Pseudouridine (psi) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, stoichiometric measurement of individual psi sites in human transcriptome remains unaddressed. Here we develop 'PRAISE', via selective chemical labeling of psi by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the psi landscape in the human transcriptome. Unlike traditional bisulfite treatment, our approach is based on quaternary base mapping and revealed an similar to 10% median modification level for 2,209 confident. 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. sites in mitochondrial mRNA catalyzed by PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide psi; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.