Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation

Pseudouridine synthases (PUSs) are responsible for the installation of pseudouridine (Ψ) modification in RNA. However, the activity and function of the PUS enzymes remain largely unexplored. Here we focus on human PUS10 and find that it co-expresses with the microprocessor (DROSHA–DGCR8 complex). Depletion of PUS10 results in a marked reduction of the expression level of a large number of mature miRNAs and concomitant accumulation of unprocessed primary microRNAs (pri-miRNAs) in multiple human cells. Mechanistically, PUS10 directly binds to pri-miRNAs and interacts with the microprocessor to promote miRNA biogenesis. Unexpectedly, this process is independent of the catalytic activity of PUS10. Additionally, we develop a sequencing method to profile Ψ in the tRNAome and report PUS10-dependent Ψ sites in tRNA. Collectively, our findings reveal differential functions of PUS10 in nuclear miRNA processing and in cytoplasmic tRNA pseudouridylation. DM-Ψ-seq, PolyA RNA-seq, rRNA(-) nuclear RNA-seq, Ribo-seq of PUS10 knockout and wild-type HEK293T cells and PAR-CLIP-seq against PUS10 in HEK293T cells.