Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
Sihao Huang, Wen Zhang, Christopher D. Katanski, Devin Dersh, Qing Dai, Karen Lolans, Jonathan W. Yewdell, A. Murat Eren, Tao Pan
Abstract
Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu) that utilizes native content training, machine learning modeling, and single-read linkage analysis. Biologically, we find interferon inducible Ψ modifications in interferon-stimulated gene transcripts which are consistent with a role of Ψ in enabling efficacy of mRNA vaccines.
Topics & Concepts
PseudouridineBiologyTranscriptomeComputational biologyMessenger RNARNANanoporeGeneNanopore sequencingInterferonRNA-SeqGene expressionGenomeGeneticsNanotechnologyMaterials scienceUridineRNA modifications and cancerRNA and protein synthesis mechanismsRNA Research and Splicing