Pseudouridylation is coupled with polyadenylation ot promote mRNA stability

Here, we developed a Ψ RNA immunoprecipitation sequencing method (Ψ-RIP-seq) combined with direct RNA sequencing by Oxford Nanopore Technologies to detect mRNA Ψ transcriptome-wide. We identified a large number of novel Ψs in mRNA, revealing a conserved enrichment of Ψ in mRNA 3′ UTR. We further showed that a genome-wide association of Ψ with mRNA polyadenylation, and uncovered that cleavage factor complex I (CFI) regulated Ψ generation in mRNA 3′ UTR. We finally demonstrated that Ψ in mRNA 3′ UTR promoted mRNA stability in a CFI-dependent manner. Examination of mRNA pseudouridylation and polyadenylation. In total, we analyzed 40 RNA samples, 28 for Ψ-RIP seq or RIP-seq, 12 for RNA-seq to examine RNA half lifetime. Each type contains at least two replicates.