Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines. Nanopore seq of two biological replicates of untreated, IFN gamma treated and IFN beta treated HeLa cells. Nanopore seq of rRNA mixture from human, yeast, C.elegans, Drosophila and stool microbiome