Integrative analysis of nanopore direct RNA sequencing data reveals a global impact of pseudouridylation on m6A and m5C modifications

We performed direct RNA sequencing from the MYCN-amplified neuroblastoma cell line BE(2)-C following depletion of the pseudouridine synthases PUS7 or DKC1. Our study identified known and novel PUS7- and DKC1-dependent pseudouridine sites in rRNA and mRNA. Furthermore, we investigated the interplay between different RNA modifications by assessing the effects of PUS7 or DKC1 depletion on m6A and m5C