Pseudouridylation is coupled with polyadenylation ot promote mRNA stability

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